Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate CA265_RS17395 CA265_RS17395 amino acid transporter
Query= TCDB::S6EX81 (469 letters) >FitnessBrowser__Pedo557:CA265_RS17395 Length = 483 Score = 301 bits (772), Expect = 2e-86 Identities = 170/456 (37%), Positives = 264/456 (57%), Gaps = 17/456 (3%) Query: 27 DFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYAEMSTVMPFAG 86 + + +GVG + +F++ G AA +GP V S+++AAL GF AL YAE ++++P AG Sbjct: 28 NLILIGVGLTLGAGLFSITGLAAANHSGPAVTLSFVIAALGCGFAALCYAEFASMIPVAG 87 Query: 87 SAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLGFHLPKVLA-NP 145 SAY++ GE F WI GW L+ EY + A V +S L + LA L +LP L +P Sbjct: 88 SAYTYSYATMGELFAWIIGWDLVLEYSVGCATVAISWSQYLTKFLASLHIYLPPQLTLSP 147 Query: 146 FGT----DG----GVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAVIAFIIVG 197 F T DG G+++I + LV++L I+ RG + ++ I+V LKV V+ FI +G Sbjct: 148 FETAKLADGSTVNGIINIPAALVVVLMTAILIRGTKGSAIVNGIIVFLKVGVVLVFIALG 207 Query: 198 ITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAKNPQKTMP 257 I PANYHP+IP + G G+SG+ G ++F +IGFD++AA++ E KNP + +P Sbjct: 208 WQYIDPANYHPYIPENTGTFGQFGWSGVLRGAGLVFFVFIGFDAVAASAQETKNPARDLP 267 Query: 258 RGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVVTAIALAG 317 GIIGSLL+ VLF V+ G+ Y +A + APV A++++ Y+ LS+ + L G Sbjct: 268 IGIIGSLLVCTVLFGLFGHVMTGLANYKEFANSGAPVAIAIEKTPYAWLSQAIILAILIG 327 Query: 318 MFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVAIVIGAFFPFA 376 +L ++A SR+ Y+ +DGLLPK ++A+ P L + + AF P Sbjct: 328 YTSVILIDLMAQSRMFYSISKDGLLPKMFSDVHAKFKTPYKSNIILCVFIGLFAAFVPMN 387 Query: 377 FLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEA--TYKMPFYPVLPALGFIGSLFVFW 434 + ++ S GTL+AF+ V +GI LR K PEA +K+PF P++P LG + + + Sbjct: 388 VVGEMTSIGTLLAFLMVCVGILILR----KTNPEAKRPFKVPFVPLIPILGILTCIAMMV 443 Query: 435 GLDVQAKLYSGIWFLIGILIYFAYGNRRSR-KSEEK 469 L + L +W +IG+ IYF YG + S+ K++E+ Sbjct: 444 FLPWETWLRLAVWLIIGLAIYFWYGKKNSKLKAQEE 479 Lambda K H 0.328 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: 624 Number of extensions: 32 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: 469 Length of database: 483 Length adjustment: 33 Effective length of query: 436 Effective length of database: 450 Effective search space: 196200 Effective search space used: 196200 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: 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