Align TRAP transporter, 4TM/12TM fusion protein (characterized, see rationale)
to candidate WP_013135013.1 ARNIT_RS06050 TRAP transporter 4TM/12TM fusion protein
Query= uniprot:E4PQE4 (729 letters) >NCBI__GCF_000092245.1:WP_013135013.1 Length = 651 Score = 352 bits (903), Expect = e-101 Identities = 209/588 (35%), Positives = 332/588 (56%), Gaps = 52/588 (8%) Query: 171 SVPDLVLIVCSLAVAAYFLV-------VYNTSMRMSTGTSFAPVGISFAAIAGTALIMEL 223 S+ +++L + SL+ Y ++ V ++ MR+S + +S I L +EL Sbjct: 62 SILNIILAILSLSTFVYMMLFEESLYSVAHSQMRLSD-----IIVVSMTII----LAIEL 112 Query: 224 TRRVAGMALVIIGLVFLAYV-FAGPYLPGFLGYPGLSVQRF-FSQVYTDAGILGPTTAVS 281 RR G + + ++ ++YV F G Y G + G+ RF + YT G+ GP +S Sbjct: 113 VRRYTGYIIPALIILSISYVLFLGQYFEGVFAFGGMDFDRFLYRMFYTGEGLFGPIATIS 172 Query: 282 STYIILFIIFAAFLQSSKVGDYFVNFAFAAAGRSRGGPAKVSIFASGLMGMINGTSAGNV 341 STY+ +FI+FAAFL S GD+ V+ + A AG+ GG V++F+S LMG I+G++ N Sbjct: 173 STYVFMFILFAAFLLKSGAGDFIVDVSNAVAGKYTGGTGHVAVFSSALMGTISGSAVANT 232 Query: 342 VSTGSLTIPLMKKVGYSKQSAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIAIA 401 VSTGS+TIP+MK+ G+ A AVEAAASTGGQIMPPIMGAGAFIMA+IT IP+ I Sbjct: 233 VSTGSITIPMMKRAGFKGTFAAAVEAAASTGGQIMPPIMGAGAFIMAQITHIPFVTIISV 292 Query: 402 AIIPAILYFASVYFMVDFEAAKTGMRGMREDELPKLRTMMKQCYLFVPIIILIVALFMGY 461 +++PAILYFAS+ F + A + ++G ++ + L + + + F+PII+L+ L GY Sbjct: 293 SVLPAILYFASISFYIHIHAKENNIKG-EDNNIKVLPLLREGFHFFIPIIVLVGLLIYGY 351 Query: 462 SVIRAGTLATVSAAVVSWLSPNK-MGLRHILQALEIASYMAIQIIVVCAAAGVIVGVISL 520 S A ++A V+ S+L+ NK MGL+ IL+AL + S + ++ + G+IVGVI++ Sbjct: 352 SPTYAASIAIVTIIFASYLTKNKRMGLKEILEALALGSQNMVVTGILLVSVGIIVGVINI 411 Query: 521 TGVGARFSVLLLDVAATSQLLALIFAMFISILLGMGMPTTAAYAVAASVVAPGLVQLGIE 580 +G+G FS L++ + S L+A+I S++LGMG+P TA+Y V + + AP LV L + Sbjct: 412 SGIGITFSQLIMAWSGNSLLIAIILIAIASLILGMGLPVTASYVVLSVLSAPALVGLMLT 471 Query: 581 P-------------------LTAHFFVFYFAVVSAITPPVALASYAAAGISGANAMETSV 621 P L+AH +F+ + S +TPPV LA++AAA I+ M+T + Sbjct: 472 PAMATLVNAGVQIPEAAMYLLSAHLIIFWLSQDSNLTPPVCLAAFAAAAIAKTPPMQTGL 531 Query: 622 ASFRIGIAAFIVPFMFFYNGALLMEAGWFEIARALVTATFGVYMLSGGVLGWFASISASW 681 S++IG +I+P +F + L+ WFE + A FG+ S + G++ Sbjct: 532 VSWKIGKGMYIIPLLFAFTP--LINGDWFERFEVFIFAFFGILSFSIVMEGFWDKKMMIL 589 Query: 682 ITRLLLIAAALLMIEGGLW-----------TDLTGIALAVLAFVIQKQ 718 + +A LL+ E + T + G + V++ ++ K+ Sbjct: 590 ERVVFAVATILLLTEDEAYHFESFFGIVQTTHIAGFIIFVVSMILHKK 637 Lambda K H 0.327 0.139 0.410 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1174 Number of extensions: 62 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 729 Length of database: 651 Length adjustment: 39 Effective length of query: 690 Effective length of database: 612 Effective search space: 422280 Effective search space used: 422280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory