Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_057508921.1 ABB28_RS12350 amino acid permease
Query= TCDB::S6EX81 (469 letters) >NCBI__GCF_001431535.1:WP_057508921.1 Length = 474 Score = 251 bits (640), Expect = 5e-71 Identities = 146/441 (33%), Positives = 231/441 (52%), Gaps = 9/441 (2%) Query: 30 ALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYAEMSTVMPFAGSAY 89 ALG+G +I IF + GQ AA AGP ++ S++LAA+ GF ALAYAE + ++P +GSAY Sbjct: 34 ALGIGAVIGGGIFVITGQAAANHAGPAIMLSFVLAAICCGFCALAYAEFAAMVPVSGSAY 93 Query: 90 SWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAPLGFHLPKVLAN----- 144 S+ FGE W GW L+ EY ++ + V ++ LL+ HLP L + Sbjct: 94 SYTYATFGELAAWFIGWMLVLEYGVSASAVAVSWTGYFLSLLSHFDIHLPAALVSAPLDG 153 Query: 145 PFGTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAVIAFIIVGITVIKPA 204 G + ++ + +++LL + + G + ++ +V+LK ++ I VG + PA Sbjct: 154 QLRPTGAIANVPAAILVLLLTWLCYVGIRKSSAMNMAMVILKTGLIVLVIAVGWKYVDPA 213 Query: 205 NYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAEAKNPQKTMPRGIIGSL 264 N+ PFI P N G G G+ G +M+F AYIGF++++ + E+ PQ+ MP G++ SL Sbjct: 214 NWQPFI-PENTGPGQFGMEGVLRGAAMVFFAYIGFEAVSVAAQESHRPQRDMPIGMMLSL 272 Query: 265 LIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSEVVTAIALAGMFIALLG 324 +I +L+ A+ V+ G+ PY+ + V L VV AL G+ +L Sbjct: 273 VICTLLYIAMAAVMTGLVPYTLLGTDEPVVTAVAAHPSLGWLRVVVEIGALVGLSSVVLV 332 Query: 325 MVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVAIVIGAFFPFAFLAQLIS 383 M++ R+ GRDGLLP K++ + P I ++ A FP L +L S Sbjct: 333 MIIGQPRIFMIMGRDGLLPPLFTKIHPKYRTPHINTVITGIGIALLAALFPLDVLGELTS 392 Query: 384 AGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGFIGSLFVFWGLDVQAKLY 443 GTLIAF V G+ LRR Q DLP +++ ++ +LG + + + + + Sbjct: 393 MGTLIAFAAVCAGVLVLRRTQ-PDLPR-PFRIRGAWLVCSLGVLSCMALLSAMTFHNWML 450 Query: 444 SGIWFLIGILIYFAYGNRRSR 464 G+W ++G IYF YG R SR Sbjct: 451 MGVWTVVGFAIYFGYGFRHSR 471 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: 623 Number of extensions: 32 Number of successful extensions: 6 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: 474 Length adjustment: 33 Effective length of query: 436 Effective length of database: 441 Effective search space: 192276 Effective search space used: 192276 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 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