/usr/share/doc/t-coffee-examples/profile1_pdb1.aln is in t-coffee-examples 11.00.8cbe486-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 | CLUSTAL FORMAT for T-COFFEE Version_4.40 [http://www.tcoffee.org], CPU=3.39 sec, SCORE=52, Nseq=9, Len=309
sp|O35205|GRAK_MOUSE M------------------------RFSSWALVSLVAGVYMSSECFHTEIIGGREVQPHS
sp|Q7YRZ7|GRAA_BOVIN M------------------NIPFPFSFPPAICLLLIPGVFPV-SC--EGIIGGNEVAPHT
sp|P03953|CFAD_MOUSE M------------------------HSSVYFVALVILGAAVCAAQPRGRILGGQEAAAHA
sp|Q9Y5K2|KLK4_HUMAN M-----------------ATAGNPWGWFLGYLILGVAGSL--VSGSCSQIINGEDCSPHS
sp|P08246|ELNE_HUMAN M------------------TLGRRLACL--FLACVLPALLLGGTALASEIVGGRRARPHA
sp|Q00871|CTRB1_PENVA MIGKLSLLLVCVAVASGNPAAGKPWHWK--SPKPL--VDPRIHVNATPRIVGGVEATPHS
sp|P08884|GRAE_MOUSE M-----------------------------PPVLILLTLLLPLGAGAEEIIGGHVVKPHS
sp|Q06606|GRZ2_RAT M-----------------------------FLFLFFLVAILPVNTEGGEIIWGTESKPHS
sp|P21844|MCPT5_MOUSE M---H-------------------------LLTLHLLLLLLGSSTKAGEIIGGTECIPHS
* *: * .*:
sp|O35205|GRAK_MOUSE RPFMASIQYRSK----HICGGVLIHPQWVLTAAHCYSWFPRGHSPTVVLGAHSLSKN-EP
sp|Q7YRZ7|GRAA_BOVIN RRYMALIK--GL----KLCAGALIKENWVLTAAHCDL----KGNPQVILGAHSTSHK-EK
sp|P03953|CFAD_MOUSE RPYMASVQVNGT----HVCGGTLLDEQWVLSAAHCMDGVTDDDSVQVLLGAHSLSAP-EP
sp|Q9Y5K2|KLK4_HUMAN QPWQAALVMENE----LFCSGVLVHPQWVLSAAHCFQ-----NSYTIGLGLHSLEADQEP
sp|P08246|ELNE_HUMAN WPFMVSLQLRGG----HFCGATLIAPNFVMSAAHCVANV-NVRAVRVVLGAHNLSRR-EP
sp|Q00871|CTRB1_PENVA WPHQAALFIDDM----YFCGGSLISSEWVLTAAHCMDGA---GFVEVVLGAHNIRQN-EA
sp|P08884|GRAE_MOUSE RPYMAFVKSVDIEGNRRYCGGFLVQDDFVLTAAHCRN-----RTMTVTLGAHNIKAK-EE
sp|Q06606|GRZ2_RAT RPYMAFIKFYDSNSEPHHCGGFLVAKDIVMTAAHCNG-----RNIKVTLGAHNIKKQ-EN
sp|P21844|MCPT5_MOUSE RPYMAYLEIVTSENYLSACSGFLIRRNFVLTAAHCAG-----RSITVLLGAHNKTSK-ED
. : *.. *: : *::**** : ** *. *
sp|O35205|GRAK_MOUSE MKQTFEIKKFIPFSRLQSGSASHDIMLIKLRTAAELNKNVQLLHLGSKN-YLRDGTKCQV
sp|Q7YRZ7|GRAA_BOVIN LDQVFSIKKAIPYPCFDPQTFEGDLQLLQLEGKATMTKAVGILQLPRTEDDVKPHTKCHV
sp|P03953|CFAD_MOUSE YKRWYDVQSVVPHPGSRPDSLEDDLILFKLSQNASLGPHVRPLPLQYEDKEVEPGTLCDV
sp|Q9Y5K2|KLK4_HUMAN GSQMVEASLSVRHPEYNRPLLANDLMLIKLDESVSESDTIRSISIASQCP--TAGNSCLV
sp|P08246|ELNE_HUMAN TRQVFAVQRIFEN-GYDPVNLLNDIVILQLNGSATINANVQVAQLPAQGRRLGNGVQCLA
sp|Q00871|CTRB1_PENVA SQVSITSTDFFTHENWNSWLLTNDIALIRLPSPVSLNSNIKTVKLPSSDVSV--GTTVTP
sp|P08884|GRAE_MOUSE TQQIIPVAKAIPHPDYNATAFFSDIMLLKLESKAKRTKAVRPLKLPRPNARVKPGDVCSV
sp|Q06606|GRZ2_RAT T-QVISVVKAKPHENYDRDSHFNDIMLLKLERKAQLNGVVKTIALPRSQDWVKPGQVCTV
sp|P21844|MCPT5_MOUSE TWQKLEVEKQFLHPKYDENLVVHDIMLLKLKEKAKLTLGVGTLPLSANFNFIPPGRMCRA
*: :::* . : :
sp|O35205|GRAK_MOUSE TGWGTTKPDLLTASDTLREVTVTIISRKRCNSQSYYNHKPVITKDMICAGDARGQKDSCK
sp|Q7YRZ7|GRAA_BOVIN AGWGSTKKDACQMSNALREANVTVIDRKICNDAQHYNFNPVIDLSMICAGGRKGEDDSCE
sp|P03953|CFAD_MOUSE AGWGVVTH-AGRRPDVLHQLRVSIMNRTTCNLRTY--HDGVVTINMMCAE--SNRRDTCR
sp|Q9Y5K2|KLK4_HUMAN SGWGLLANG--RMPTVLQCVNVSVVSEEVCSKL----YDPLYHPSMFCAGGGQDQKDSCN
sp|P08246|ELNE_HUMAN MGWGLLGRNR-GIASVLQELNVTVVTS-LCR------------RSNVCTLVRGRQAGVCF
sp|Q00871|CTRB1_PENVA TGWGRPSDSASGISDVLRQVNVPVMTNADCDSVYGI-----VGDGVVCIDG-TGGKSTCN
sp|P08884|GRAE_MOUSE AGWGSRSINDTKASARLREAQLVIQEDEECKKRFRH----YTETTEICAGDLKKIKTPFK
sp|Q06606|GRZ2_RAT AGWGRLAN--CTSSNTLQEVNLEVQKGQKCQDMSED----YNDSIQLCVGNPSEGKATGK
sp|P21844|MCPT5_MOUSE VGWGRTNVNE-PASDTLQEVKMRLQEPQACKHFTS-----FRHNSQLCVGNPKKMQNVYK
*** . *: : : * .*
sp|O35205|GRAK_MOUSE GDSGGPLICKGIFHALVSQGYK-CGIAKKPGIYTLLTKKYQTWIKSKLAPSR--------
sp|Q7YRZ7|GRAA_BOVIN GDSGSPLICDNVFRGVTSFGK--CGNPQKPGIYILLTKKHLNWIKKTIAGAI--------
sp|P03953|CFAD_MOUSE GDSGSPLVCGDAVEGVVTWGSRVCGNGKKPGVYTRVSS-YRMWIENITNGNM--------
sp|Q9Y5K2|KLK4_HUMAN GDSGGPLICNGYLQGLVSFGKAPCGQVGVPGVYTNLCK-FTEWIEKTVQAS---------
sp|P08246|ELNE_HUMAN GDSGSPLVCNGLIHGIASFVRGGCASGLYPDAFAPVAQ-FVNWIDSIIQRSEDNPCPHPR
sp|Q00871|CTRB1_PENVA GDSGGPLNLNGMTYGITSFGSSAGCEKGYPAAFTRVYY-YLDWIQQKTGVTP--------
sp|P08884|GRAE_MOUSE GDSGGPLVCDNKAYGLLAYAKNRT---ISSGVFTKIVH-FLPWISRNMKLL---------
sp|Q06606|GRZ2_RAT GDSGGPFVCDGVAQGIVSYRLCTG---TLPRVFTRISS-FIPWIQKTMKVLQ--------
sp|P21844|MCPT5_MOUSE GDSGGPLLCAGIAQGIASYVHRNA---KPPAVFTRISH-YRPWINKILREN---------
****.*: . .: : . : : . **.
sp|O35205|GRAK_MOUSE -------AH
sp|Q7YRZ7|GRAA_BOVIN ---------
sp|P03953|CFAD_MOUSE -------TS
sp|Q9Y5K2|KLK4_HUMAN ---------
sp|P08246|ELNE_HUMAN DPDPASRTH
sp|Q00871|CTRB1_PENVA ---------
sp|P08884|GRAE_MOUSE ---------
sp|Q06606|GRZ2_RAT -------QS
sp|P21844|MCPT5_MOUSE ---------
|