Align TRAP transporter (characterized, see rationale)
to candidate WP_013135076.1 ARNIT_RS06360 TRAP transporter permease DctM/Q
Query= uniprot:A8LI82 (743 letters) >NCBI__GCF_000092245.1:WP_013135076.1 Length = 599 Score = 319 bits (818), Expect = 2e-91 Identities = 189/529 (35%), Positives = 296/529 (55%), Gaps = 15/529 (2%) Query: 187 VLAICGVAVATYLITIYGTLMRNSTGTPFAPIGISIAAVAGTALIMELTRRVAGMALIVI 246 +L +CG+ + Y++ Y L + G+ + +A ++ ++E+ RR +AL + Sbjct: 72 ILLVCGLFSSLYIVFNYSVL-EDQYGSLEGYLQYFVA-LSLILSVLEMARRAIKLALPLT 129 Query: 247 AGIFLAYVFVGQYLPGFLNAPAVTWQRFFSQ-VYTDAGILGPTTAVSSTYIILFIIFAAF 305 A I LAY G Y+PG + FF V + GI G T VS + +F+I AF Sbjct: 130 ATIALAYGLWGHYIPGNFGHQEIPMDSFFGTLVIAEGGIFGALTGVSVNVVAVFVILGAF 189 Query: 306 LQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTIPLMKK 365 + + G+ F++ + AG+ RGG AKV++ AS G I+G+++ NV +TG+ TIP MK+ Sbjct: 190 VGIGEGGNAFMSLSTKIAGRLRGGAAKVSVLASAFFGSISGSASANVASTGAFTIPTMKR 249 Query: 366 VGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFVSVY 425 + Y AGA EA ASTGGQIMPP+MGAGAFIMAE+ G+PY +I AI PAIL+FV+V+ Sbjct: 250 LKYPASLAGATEAVASTGGQIMPPLMGAGAFIMAELLGVPYAKIMATAIFPAILFFVTVW 309 Query: 426 FMVDLEAAKLGMRGMSRDELPKFNKMVRQVYLFL-PIIILIYAL-FMGYSVIRAGTLATV 483 +D+ A K + M ++++PK N +++ FL P IL+YAL +G + + LA Sbjct: 310 IGIDVFAKKYNLLAMDKEDIPKLNLVLKLAPFFLIPFGILLYALIIVGKTPQYSAALAIF 369 Query: 484 AAAVV-----SWFTPFRMGPRSIAKAFEIAGTMSVQIIAVCACAGIIVGVISLTGVGARF 538 A+ ++ W F+ A I +V CAGI++GV+++TG+G + Sbjct: 370 ASIILLLVNRDWKISFKEFIEKFVDGCITASRQIASIASVIICAGIVIGVLNITGIGVKI 429 Query: 539 SAVLLGIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPGLVQLGIPLLTAHFF 598 ++ +L +++ +AL ++LGM +PTTAAY + S+ P L + G+ + AH F Sbjct: 430 TSAILYLSNGQLFVALLLTAVACLILGMEVPTTAAYIICVSIAGPTLQEYGLSAIQAHLF 489 Query: 599 VFYFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIGIAAFIVPFMFFYNSAIL-MD 657 VF+FA+LS ITPPV + A+GI+ AN +E + S K+GI +IVP F N ++ D Sbjct: 490 VFWFALLSTITPPVCGTVFIASGIAQANWIEVAGKSMKLGIGLYIVPLAFVVNPFLIEPD 549 Query: 658 GTWFEVLRAGATAVVGVFFLSSGVQGWFMGGRAAWFLRVGLVFAALMLI 706 + + VG+ LS+ + + + LRVGLV L+ I Sbjct: 550 TNFLYAFLSFIKIAVGLGLLSNAL----VNDKQKAVLRVGLVLLGLITI 594 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: 1135 Number of extensions: 80 Number of successful extensions: 4 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: 743 Length of database: 599 Length adjustment: 38 Effective length of query: 705 Effective length of database: 561 Effective search space: 395505 Effective search space used: 395505 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