Align TRAP transporter (characterized, see rationale)
to candidate WP_006748820.1 THITH_RS04915 DUF3394 domain-containing protein
Query= uniprot:A8LI82 (743 letters) >NCBI__GCF_000227685.2:WP_006748820.1 Length = 910 Score = 224 bits (572), Expect = 1e-62 Identities = 137/368 (37%), Positives = 204/368 (55%), Gaps = 32/368 (8%) Query: 79 RIVHIAGALALGFLLFAARTDFPGPGKETPLLGYVAYGLMVPALFSLGMAASFSMEIASG 138 R +H+A A+ L FLLF AR +P+ +AA F + +A G Sbjct: 68 RSIHLAFAVFLAFLLFPAR---------------------LPSRHGPHIAAGFYLLLALG 106 Query: 139 VMWNGIDEGIKFNETWLFGLPLIVATAG-GIVLSWFHKRARSGFSAP--DLVLAICGVAV 195 +W + + + W+ P+ + G + L+W R P D +LA Sbjct: 107 -LWLLAWQQHQAEQPWV---PVYLLIGGVALALAWPAWRPAPLERIPWIDWLLAFAAALT 162 Query: 196 ATYLITIYGTLMRNSTGTPFAPIGISIAAVAGTALIMELTRRVAGMALIVIAGIFLAYVF 255 A YL + L + G P + IAA G L++E TRRV G AL+VIAG+FL Y F Sbjct: 163 AGYLFLFHQELAQRP-GRPI--LADMIAAGLGMLLLLEATRRVLGPALMVIAGVFLLYTF 219 Query: 256 VGQYLPGFLNAPAVTWQRFFSQVY-TDAGILGPTTAVSSTYIILFIIFAAFLQASKVGDY 314 G ++P L ++ R SQ + ++ G+ G VS++++ LF++F A L+ + G Y Sbjct: 220 AGPWMPDVLAHRGASFGRAMSQQWLSNEGVFGIALGVSTSFVFLFVLFGALLERAGAGGY 279 Query: 315 FVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTIPLMKKVGYHKKTAG 374 F+ AFA G RGGPAK A+ ASGL G+++G+S NVV TG+ T+PLMK+ G+ AG Sbjct: 280 FIRVAFALLGHLRGGPAKAAVVASGLTGVVSGSSIANVVTTGTFTVPLMKRTGFPAAKAG 339 Query: 375 AVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFVSVYFMVDLEAAK 434 AVE A+S GQ+MPP+MGA AF+M E GIPY E+ A +PA++ ++++ ++V LEA K Sbjct: 340 AVEVASSVNGQLMPPVMGAAAFLMVEYVGIPYVEVIKHAFLPALIAYLALLYIVHLEACK 399 Query: 435 LGMRGMSR 442 G+ G+ R Sbjct: 400 SGLEGLPR 407 Score = 125 bits (314), Expect = 1e-32 Identities = 81/285 (28%), Positives = 143/285 (50%), Gaps = 26/285 (9%) Query: 455 VYLFLPIIILIYALFM-----GYSVIRA-----GTLATVAAAVVSW------FTPFRMGP 498 ++ LP+++LI+AL + G S A G L T ++ + G Sbjct: 496 LHYLLPVVVLIWALVVERLSPGLSAFWAVLFLIGILLTQRPLMLFFRGRRGHLQAAMAGV 555 Query: 499 RSIAKAFEIAGTMSVQIIAVCACAGIIVGVISLTGVGARFSAVLLGIADTSQLLALFFAM 558 + + + I A AGIIVG +++TG+G + ++ ++ LL L Sbjct: 556 HDLGQGLVQGARNMIGIGVATAAAGIIVGTVAMTGIGLVMTDLVEWLSGGHLLLMLLLTA 615 Query: 559 CIAILLGMGMPTTAAYAVAASVVAPGLVQLG------IPLLTAHFFVFYFAVLSAITPPV 612 I ++LG+G+PTTA Y + A+++AP +V L IPL+ AH FVFYF +++ +TPPV Sbjct: 616 VICLVLGLGLPTTANYIIVATLMAPVIVDLAAQNDLLIPLIAAHLFVFYFGIMADVTPPV 675 Query: 613 ALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAILM---DGTWFEVLRAGAT 669 LAS+AAA ++ A+P+ T + +F + +PF+F +N+ +L+ D W ++ Sbjct: 676 GLASFAAAAVARADPIRTGIQAFWYSLRTVTLPFVFVFNTQLLLIGVDNLW-QLTLTFFG 734 Query: 670 AVVGVFFLSSGVQGWFMGGRAAWFLRVGLVFAALMLIEGGIMSDL 714 ++ G+ + Q + + W + L+ A +L+ G M L Sbjct: 735 SLAGILVFVAATQHYLLVRNRVWETALLLLVALTLLVPGVWMDRL 779 Lambda K H 0.327 0.140 0.419 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: 1794 Number of extensions: 122 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 743 Length of database: 910 Length adjustment: 42 Effective length of query: 701 Effective length of database: 868 Effective search space: 608468 Effective search space used: 608468 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: 56 (26.2 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