Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_047094595.1 AAV99_RS13360 amino acid permease
Query= TCDB::S6EX81 (469 letters) >NCBI__GCF_001013305.1:WP_047094595.1 Length = 529 Score = 229 bits (585), Expect = 1e-64 Identities = 150/484 (30%), Positives = 245/484 (50%), Gaps = 41/484 (8%) Query: 17 KHYNQVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVALAYA 76 K ++ L + G+G II T IF L AQ AGPG++ ++++A V AL YA Sbjct: 19 KSLHRTLGAFQLMLFGIGCIIGTGIFVLTA-AGAQKAGPGLMLAFVIAGTVCIVAALCYA 77 Query: 77 EMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLA--PL 134 E+++++P AGSAY++ GE W GWAL+ EY IA + V G+S + Sbjct: 78 EIASMIPVAGSAYTYSYATVGEFIAWTVGWALVLEYAIAASAVSVGWSGYFAGTILGDTF 137 Query: 135 GFHLP-KVLANPF---GTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVAAV 190 G LP + A P G GG +++ ++++ LL ++ G S++ +++ +LV++KV A+ Sbjct: 138 GISLPVSLTAGPLALGGAPGGFINLPAMVIALLVTWLLMIGTSESAKVNAVLVLIKVTAL 197 Query: 191 IAFIIVGIT--VIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAE 248 AFI + +T A ++PF+P G+G G + IF AY+GFD+++ + E Sbjct: 198 TAFIALTLTSSEFDVARFNPFLPA-GVFGGWGTGVGAVGAAATIFFAYVGFDAVSTAAEE 256 Query: 249 AKNPQKTMPRGIIGSLLIAVV---LFAAVTLVLVGMHPYSAYAGNAAPVG---------- 295 KNPQ+ +P G++GSLL V L AA + +G P G P G Sbjct: 257 TKNPQRNVPIGLVGSLLFCTVFYILVAAGAIGTIGGQPIMGPGGIPFPAGSEELARQCAL 316 Query: 296 ---------------WALQQSGYSVLSEVVTAIALAGMFIALLGMVLAGSRLLYAFGRDG 340 L++ G+ + V+ A+ + +L ++ A +R+ + RDG Sbjct: 317 PQFSDALVCSNEALAHVLREIGFGAIGNVLGYAAILALPSVILVLLFAQTRIFFVMSRDG 376 Query: 341 LLPKGLGKMNARNLPANGVWTLAIVAIVIG-AFFPFAFLAQLISAGTLIAFMFVTLGIYS 399 LLP+GL K++ + V + V + IG AFFP LA + +AGTL AF V + + Sbjct: 377 LLPEGLSKVHPKWKTPYVVTAITGVIVAIGAAFFPVGQLADIANAGTLYAFAMVAVAVMV 436 Query: 400 LRRRQGKDLPEATYKMPFYPVLPALGFIGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYG 459 LRR ++++P ++ + +G +F+F L ++A L +W LIG +IYF Y Sbjct: 437 LRRTD--PTRTRSFRVPALMIIGPVTVLGCVFLFLNLPLEAMLVLPVWTLIGCVIYFGYS 494 Query: 460 NRRS 463 S Sbjct: 495 RGSS 498 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: 700 Number of extensions: 39 Number of successful extensions: 5 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: 529 Length adjustment: 34 Effective length of query: 435 Effective length of database: 495 Effective search space: 215325 Effective search space used: 215325 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: 52 (24.6 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