Align High-affinity branched-chain amino acid transport system permease protein BraE, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate WP_028998314.1 H537_RS0113280 branched-chain amino acid ABC transporter permease
Query= TCDB::P21628 (417 letters) >NCBI__GCF_000430725.1:WP_028998314.1 Length = 311 Score = 172 bits (435), Expect = 2e-47 Identities = 107/328 (32%), Positives = 169/328 (51%), Gaps = 25/328 (7%) Query: 92 RWAVLALVVVAFVWPFFASRG-AVDIATLILIYVMLGIGLNIVVGLAGLLDLGYVGFYAV 150 R +LAL V + P A+DIA + + + IGLN+++G AG + +G+ F A+ Sbjct: 7 RPGLLALATVLLLLPLVLPNNYALDIAVRVALAAVAVIGLNLLMGFAGQISIGHAAFVAI 66 Query: 151 GAYTYALLAEYAGFGFWTALPIAGMMAALFGFLLGFPVLRLRGDYLAIVTLGFGEIIRIL 210 GAY L ++ + ++ +A + AAL +L+ P+LRL+G L + TLG G I+ ++ Sbjct: 67 GAYGSGLATQHLAWSPLLSVAVAALGAALVAWLIAKPILRLKGHPLTMATLGLGIIVNMV 126 Query: 211 LRNMTEITGGPNGIGSIPKPTLFGLTFERRAPEGMQTFHEFFGIAYNTNYKVILLYVVAL 270 L N +GGP+G+ +P + G F KV+ YV+A Sbjct: 127 LINEVSWSGGPDGV-PVPPLMVAGFVFA----------------------KVLHWYVLAA 163 Query: 271 LLVLLALFVINRLMRMPIGRAWEALREDEVACRALGLNPTIVKLSAFTIGASFAGFAGSF 330 +L+L A+ + L P GRA L EVA R G++ K+ AF A FA +GS Sbjct: 164 VLLLAAVVLSLNLFESPAGRALRGLNSSEVAARVAGVDVGSFKVRAFVASAVFASVSGSL 223 Query: 331 FAARQGLVTPESFTFIESAMILAIVVLGGMGSQLGVILAAVVMVLL-QEMRGFNEYRMLI 389 G ++P F S + +VVLGGMGS G +L A ++ LL Q + G Y M++ Sbjct: 224 TGHYLGFISPALSAFTHSVELATMVVLGGMGSTFGAVLGAALLTLLPQLLGGLQGYEMIL 283 Query: 390 FGLTMIVMMIWRPQGLLPMQRPHLELKP 417 FGL +++ M++ P+GL+P L+ +P Sbjct: 284 FGLILMLTMMFLPKGLVPSLALRLQRRP 311 Lambda K H 0.330 0.146 0.439 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: 380 Number of extensions: 28 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: 417 Length of database: 311 Length adjustment: 29 Effective length of query: 388 Effective length of database: 282 Effective search space: 109416 Effective search space used: 109416 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 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