COMPASS


This is an example of COMPASS output produced by running this query against PDB database
COMPASS 3.0
Reference:
Ruslan I. Sadreyev and Nick V. Grishin (2003) COMPASS: a tool for comparison
of multiple protein alignments with assessment of statistical significance.
J Mol. Biol. 326(1):317-36
Job ID: JOB_unRIK0

Query = QUERY  Input processed by alignment reader (please check!)
length=173; filtered_length=173; Neff=3.017
(threshold of effective gap content in columns: 0.5)

Database: PDB70_iter5
Effective database length used: 3663686

COMPASS alignment format: CAPITAL letters: residues at positions aligned by COMPASS (input alignment positions with gap content < 0.5) lower-case letters: residues at positions not used by COMPASS (input alignment positions with gap content >= 0.5) '-' : gaps retained from original alignments at positions aligned by COMPASS (positions with gap content < 0.5) '.' : gaps retained from original alignments at positions not used by COMPASS (positions with gap content >= 0.5) '=' : gaps introduced by COMPASS in profile-profile alignment '~' : gaps introduced by COMPASS against positions that are not used in the construction of profile-profile alignment (positions with gap content >= 0.5) Clickable sequence names: links to full alignments. For more details, see documentation.
Hits with E-value BETTER than threshold: Profiles producing significant alignments: Score E-value 2F6SA Structure Of Cell Filamentation Protein (Fic) From He 391 0.00e+00 2G03A Structure Of A Putative Cell Filamentation Protein Fr 405 0.00e+00 3CUCA Crystal Structure Of Protein Of Unknown Function With 122 7.15e-10
Hits with E-value WORSE than threshold (may be not biologically meaningful): 2A0ZA The Molecular Structure Of Toll-Like Receptor 3 Ligan 72 9.39e-02 2QC0A Crystal Structure Of Uncharacterized Protein (Np_7197 69 1.89e-01
Alignments:

Subject = 2F6SA Structure Of Cell Filamentation Protein (Fic) From He Structure  Next 10

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Database links:    PDB     SCOP     CATH     NCBI


Query  
Subjct  
length=180 filtered_length=160 Neff=14.512 Smith-Waterman score = 391 Evalue = 0.00e+00 2F6S-A 2 RQSLEKAKHLIQSGLIDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNIAKGNFRFANC 61 CONSENSUS_1 2 RLSKKKAKELFDSGLLDTLEIGTFKGLADIHKYLFGDLYDFAGKIRDVNIAKGNFRFAPL 61 +L++K+A+EL++SGLLD+LE+GT+KGL++IH++LFGD+YD+AGK+R+VNI+KG+FRFAP+ CONSENSUS_2 7 ILELKNALELIESGLLDELEPGTLKGLKEIHRLLFGDIYDWAGKFRTVNISKGGFRFAPP 66 2F6SA 7 RQSLEKAKHLIQSGLIDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNIAKGNFRFANC 66 2F6S-A 62 LYLDLILPRIESXPQNNFNQIVEKYVEXNIAHPFLEGNGRATRIWLDLLLKKELKKIVLW 121 CONSENSUS_1 62 LFLDLALKKIDKLPENTFDEIIEKYVEMNIAHPFREGNGRATRIWLDLLLKKELKKVVDW 121 +++++ L++++KL+++TF+E++E+++E+N++HPFR+GNGR++R++L+LLLKK+++K++DW CONSENSUS_2 67 EYIEPLLDELEKLKQETFEELAEFHAELNVIHPFRDGNGRTGRLLLNLLLKKAGGKPIDW 126 2F6SA 67 LYLDLILPRIESMPQNNFNQIVEKYVEMNIAHPFLEGNGRATRIWLDLLLKKELKKIVLW 126 2F6S-A 122 DRIDKAAYLSAXERSPVNDLEIKTLLKKHL~SSNTNDPLTLI 162 CONSENSUS_1 122 SRIDKDDYLLAMERSPVDDLELKHLLKKAL~TDKINDREVFL 162 S++DK++YL+A+ERSPV+DLELK+LLKKA TD+IN+REVF+ CONSENSUS_2 127 SKVDKEEYLEALERSPVKDLELKFLLKKA=.TDLINNREVFI 167 2F6SA 127 DRIDKAAYLSAMERSPVNDLEIKTLLKKH=lSSNTNDPLTLI 167
Subject = 2G03A Structure Of A Putative Cell Filamentation Protein Fr Structure

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Downloads:        PDB file    PyMOL

Database links:    PDB     SCOP     CATH     NCBI


Query  
Subjct  
length=177 filtered_length=162 Neff=14.531 Smith-Waterman score = 405 Evalue = 0.00e+00 2F6S-A 2 RQSLEKAKHLIQSGLIDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNIAKGNFRFANC 61 CONSENSUS_1 2 RLSKKKAKELFDSGLLDTLEIGTFKGLADIHKYLFGDLYDFAGKIRDVNIAKGNFRFAPL 61 +L++++AK+LF+SGLLD+LE+GT+KGL++IH++LFGDLYD+AGK+R+VNI+KG+F+FAP CONSENSUS_2 6 ELELENAKALFESGLLDELEPGTLKGLKEIHRLLFGDLYDWAGKFRTVNISKGGFVFAPP 65 2G03A 6 EQSLHNARRLFESGDIDRIEVGTTAGLQQIHRYLFGGLYDFAGQIREDNISKGGFRFANA 65 2F6S-A 62 LYLDLILPRIESXPQNNFNQIVEKYVEXNIAHPFLEGNGRATRIWLDLLLKKELKKIVLW 121 CONSENSUS_1 62 LFLDLALKKIDKLPENTFDEIIEKYVEMNIAHPFREGNGRATRIWLDLLLKKELKKVVDW 121 ++L++ L++++KL+E++F+E++E+++E+N++HPFR+GNGR++R++LDL+L+KE+++++DW CONSENSUS_2 66 EYLEDLLEELEKLDEELFEELAEFHAELNVIHPFRDGNGRTGRLLLDLILAKEAGYPLDW 125 2G03A 66 MYLKEALVKIEQMPERTFEEIIAKYVEMNIAHPFLEGNGRSTRIWLDLVLKKNLKKVVNW 125 2F6S-A 122 DRIDKAAYLSAXERSPVNDLEIKTLLKKHLSSNTNDPLTLIK 163 CONSENSUS_1 122 SRIDKDDYLLAMERSPVDDLELKHLLKKALTDKINDREVFLK 163 SRIDK++YL+A++RSPV+DLELK+LLKKALTDKINDREVFLK CONSENSUS_2 126 SRIDKEEYLEALIRSPVGDLELKELLKKALTDKINDREVFLK 167 2G03A 126 QNVSKTLYLQAMERSPVNDLELRFLLKDNLTDDVDNREIIFK 167
Subject = 3CUCA Crystal Structure Of Protein Of Unknown Function With Structure

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Downloads:        PDB file    PyMOL

Database links:    PDB     SCOP     CATH     NCBI


Query  
Subjct  
length=262 filtered_length=254 Neff=18.039 Smith-Waterman score = 122 Evalue = 7.15e-10 2F6S-A 3 QSLEKAKHLIQSGLIDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKN===IAKGNFRFA 59 CONSENSUS_1 3 LSKKKAKELFDSGLLDTLEIGTFKGLADIHKYLFGDLYDFAGKIRDVN===IAKGNFRFA 59 L K+A EL ++ L + E T + + ++H+ L+++L+++AG++R+ + I++G F+++ CONSENSUS_2 71 LNHKEALELILELLKSKEEPLTEDLILELHRLLLRGLLEDAGEFRRRDNVIIGGGVFVPP 130 3CUCA 71 KAHNVGLEMIKQEAQDKERPLTESFIRELNRTILVQDYWKVGEYKSRPNSVLTGEVFSYA 130 2F6S-A 60 NCLYLDLILPRIESXPQNNFNQIVEKYVEXNI========AHPFLEGNGRATRIWLDLLL 111 CONSENSUS_1 60 PLLFLDLALKKIDKLPENTFDEIIEKYVEMNI========AHPFREGNGRATRIWLDLLL 111 P +++ L+++ ++ +++ D+ + +++ + +HPF++GNGR +R++L+LLL CONSENSUS_2 131 PPEEVPALLEELLDWLNSEEDKGDLDPLIRAALLHFRFVYIHPFLDGNGRTGRLLLNLLL 190 3CUCA 131 SPEETPAFMTSLVDWYNLEADKGILTPVELAALLHYRYIRIHPFEDGNGRIARLLVNFVL 190 2F6S-A 112 KKELKKIVLWDRIDKAAYLSAXERSPVNDLEIKTLLKKHLSSNTNDPLTLI=KGITQSY 169 CONSENSUS_1 112 KKELKKVVDWSRIDKDDYLLAMERSPVDDLELKHLLKKALTDKINDREVFL=KGIDASY 169 ++ ++ + + D+D+Y++A+E++ V L ++ ++ ++++ + F+ +++++S+ CONSENSUS_2 191 LRAGYPLSIIIKEDRDEYYDALEAADVGGLGDLDGRWNLNEGDLTPFIEFFLEALEESL 249 3CUCA 191 HRYGYPMIVIHSEDKSNYLNILHQCDVEAGLTPSDGANATLNDILPFVNYLSSCLIRSL 249
Subject = 2A0ZA The Molecular Structure Of Toll-Like Receptor 3 Ligan Structure
length=671 filtered_length=668 Neff=20.855 Smith-Waterman score = 72 Evalue = 9.39e-02 2F6S-A 17 IDTIEVGTIKGLQEIHRFLFEGLYEFAGKIRDKNIAKGNFRFAN===========CLYLD 65 CONSENSUS_1 17 LDTLEIGTFKGLADIHKYLFGDLYDFAGKIRDVNIAKGNFRFAP===========LLFLD 65 L +L + K L++++ L+G+L ++R ++++ +++++ + L+L+ CONSENSUS_2 539 LKVLDLSGNK=LSGLPPGLLGGLT====SLRVLDLSGNRLSGLIPGLLGNLTSLEVLDLS 593 2A0ZA 539 LHILNLESNG=FDEIPVEVFKDLF====ELKIIDLGLNNLNTLPASVFNNQVSLKSLNLQ 593 2F6S-A 66 LILPRIESXPQNNFNQIVEKYVEXNIAHPFLEGNGRATRIWLDLLLKKELKKIVLWDRID 125 CONSENSUS_1 66 LALKKIDKLPENTFDEIIEKYVEMNIAHPFREGNGRATRIWLDLLLKKELKKVVDWSRID 125 + K+ L+++++ +++ + +++ + +++ ++++ LD+L +++++++ + +++ CONSENSUS_2 594 NN==KLSGLIPSLLGDLLSSLSVLDLSGNPLLCDCDNLGWFLDWLNESNVTLPGLADDV= 650 2A0ZA 594 KN==LITSVEKKVFGPAFRNLTELDMRFNPFDCTCESIAWFVNWINETHTNIPELSSHY= 650 2F6S-A 126 KAAYLSAXERSPVNDLEI 143 CONSENSUS_1 126 KDDYLLAMERSPVDDLEL 143 + ++++++++ P+ DL+L CONSENSUS_2 651 LCASPPSLRGKPLLDLDL 668 2A0ZA 651 LCNTPPHYHGFPVRLFDT 668
Subject = 2QC0A Crystal Structure Of Uncharacterized Protein (Np_7197 Structure
length=367 filtered_length=353 Neff=16.986 Smith-Waterman score = 69 Evalue = 1.89e-01 2F6S-A 28 LQEIHRFLFEGLYEF===AGKIRDKNIAKGNFRFANCLY==LDLILPRIESXPQNNFN== 80 CONSENSUS_1 28 LADIHKYLFGDLYDF===AGKIRDVNIAKGNFRFAPLLF==LDLALKKIDKLPENTFD== 80 + ++H+ L++++ ++ G++R+ ++ G + F P + L++ L+++++ +++ D CONSENSUS_2 122 ILELHRLLLSGGRGERKVPGEFRRSQNTGGIVHFPPPPPELLPELLDDLEDFLNDEDDLD 181 2QC0A 122 ALEICSTIKSVQMDVRKVPGTSLTNQATGEVIYTPPAGESVIRDLLSNWEAFLHNQDDVD 181 2F6S-A 81 ===QIVEKYVEXNIAHPFLEGNGRATRIWLDLLLKKE 114 CONSENSUS_1 81 ===EIIEKYVEMNIAHPFREGNGRATRIWLDLLLKKE 114 +++ ++++ HPF++GNGR +R++++LLL ++ CONSENSUS_2 182 PLIRAALAHFQFETIHPFLDGNGRIGRLLITLLLARK 218 2QC0A 182 PLIKMAMAHYQFEAIHPFIDGNGRTGRVLNILYLIDQ 218
Parameters: E-value cutoff: 1.000e+00 Maximal number of hits to display: 100 Lambda_ungapped: 3.1760e-01 Expected value of positional scores: -5.2090e-01 Gap opening: 10 Gap extension: 1