Align FcbT3, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized)
to candidate HSERO_RS13470 HSERO_RS13470 C4-dicarboxylate ABC transporter
Query= TCDB::Q9RBQ9 (439 letters) >FitnessBrowser__HerbieS:HSERO_RS13470 Length = 449 Score = 231 bits (590), Expect = 3e-65 Identities = 146/445 (32%), Positives = 239/445 (53%), Gaps = 31/445 (6%) Query: 14 TTVLLFLGLPVAYSFFAINVV--GAWLFLGGDSALGQLVRNGLVAVASFSLTPIPLFILM 71 T V++ G+P+A FA+ VV G F +S+L + +N +AS +L IPLFIL Sbjct: 14 TIVVMCSGMPIA---FALGVVATGFMYFFMPESSLDTITQNVYEEIASITLLSIPLFILK 70 Query: 72 GELLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLMLPM 131 G + + + I + ++PG L + V A F+A++GS+ AT + +GS +P Sbjct: 71 GAAIGKSPAGKDLYSAIHAWLNKVPGGLGIANVFACALFAAMAGSSPATCSAIGSAGIPE 130 Query: 132 MLARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLLAISF 191 M RGY P G I A G + +L+PPS +L A S+ +L + G+ PG+LL + F Sbjct: 131 MRRRGYSPGFAAGIIAAGGTLGILLPPSITMILYAVAAEQSLGRLFLAGIGPGVLLVLLF 190 Query: 192 VAYIVASAKLRPESAPREELVVLRGWERWR-------------ELVVYVLPLSLIFVAIV 238 Y V A+ A V G + E++ VLP ++ + ++ Sbjct: 191 AGYAVYRARKEYRLA---HAVYSAGGAKSAYLDDEHFTLAQKVEMLPRVLPFLILLIGVM 247 Query: 239 AVISGGVATPTEAAAIGCAATLA-ITLMYRALRWQSLVQALQGTVAISGMILFIIVAATT 297 + GG+ATP+E A +G L I ++YR + + + L T+ SGM+L II + Sbjct: 248 VALYGGLATPSETAGLGALLALVLIAVVYRIYKPREIAPFLSSTIKESGMLLLIIGMSLL 307 Query: 298 FSQVLSF----SGATNGIVDLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFY 353 +S V+S+ A +VDL S L ++A++L ++I LG F+ VS++L+T P Sbjct: 308 YSYVMSYLHISQSAAQWVVDLHLSKWL----LLAVILGMVIVLGFFLPPVSIILMTAPII 363 Query: 354 MPIVKSLGIDQIWFGVMYLICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVG 413 +P +K+ G D IWFG++ + M++GL+ PP G+ L+ +K +AP I +G V +P++ Sbjct: 364 LPPLKAAGFDLIWFGIVMTVVMEMGLIHPPVGLNLFVIKNIAP-DIALGDVIKGTIPFLA 422 Query: 414 LSFTMLILIFFWPGIATWLPDVFVG 438 L F ++L+ +PGIAT LPD+ +G Sbjct: 423 LMFLAVLLLCMFPGIATLLPDLLMG 447 Lambda K H 0.329 0.143 0.433 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: 500 Number of extensions: 35 Number of successful extensions: 3 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: 439 Length of database: 449 Length adjustment: 32 Effective length of query: 407 Effective length of database: 417 Effective search space: 169719 Effective search space used: 169719 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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