Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate WP_090443593.1 BLS63_RS10635 TRAP transporter large permease
Query= uniprot:Q88NP0 (426 letters) >NCBI__GCF_900100495.1:WP_090443593.1 Length = 317 Score = 260 bits (664), Expect = 5e-74 Identities = 137/314 (43%), Positives = 198/314 (63%), Gaps = 2/314 (0%) Query: 110 SVADTASVGSVLIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIA 169 S A A+VGS+ I M R GYP+ F + + +L PPS V+Y AA S+ Sbjct: 1 SPATVAAVGSIAIAGMVRSGYPQAFGAGIVCNAGTLGILIPPSIVMVVY--AAATETSVG 58 Query: 170 SLFMAGIMPGLLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILG 229 LFMAG++PG+LL V+M I A+K N P LRE L A EA+WGL+ MVIILG Sbjct: 59 KLFMAGVVPGILLGVVLMTAIYIIARKMNLPALPRASLRELLSTAREAIWGLLLMVIILG 118 Query: 230 GILSGVFTATESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASF 289 GI SG+FT TE+AAVA V++ FV +F+Y+D + R+ PK++ + + ++M +I A F Sbjct: 119 GIYSGMFTPTEAAAVAAVYAGFVALFVYKDMRIRECPKVLLESGKLSIMLMFIIANAMLF 178 Query: 290 GYVMTLMQIPSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVIT 349 +V+T QIP IT + + + L+ +N +L++ G M+ + +ILIL PIL P+ Sbjct: 179 AHVLTTEQIPQTITAWVIEMGLQPWQFLLVVNLVLLVAGAFMEPSAIILILAPILFPIAV 238 Query: 350 GIGVDPVHFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLM 409 +G+DP+H G+IM+VN+ IGLITPPVG LFV SA+ + + + +KA P+ + L L+ Sbjct: 239 QLGIDPIHLGIIMVVNMEIGLITPPVGLNLFVTSAVTGMPLTAVIKAAWPWLMLLLSFLV 298 Query: 410 AVTYIPAISLWLPS 423 +TYIPAISL LP+ Sbjct: 299 VITYIPAISLALPN 312 Score = 27.7 bits (60), Expect = 5e-04 Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 2/71 (2%) Query: 355 PVHFGMIMLVNLG-IGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTY 413 P FG ++ N G +G++ PP V+ V +A + S+ A + + L +VLM Y Sbjct: 22 PQAFGAGIVCNAGTLGILIPP-SIVMVVYAAATETSVGKLFMAGVVPGILLGVVLMTAIY 80 Query: 414 IPAISLWLPSV 424 I A + LP++ Sbjct: 81 IIARKMNLPAL 91 Lambda K H 0.329 0.142 0.418 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: 408 Number of extensions: 19 Number of successful extensions: 3 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: 426 Length of database: 317 Length adjustment: 30 Effective length of query: 396 Effective length of database: 287 Effective search space: 113652 Effective search space used: 113652 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 (21.8 bits) S2: 49 (23.5 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