Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate Ac3H11_4169 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4169 Length = 383 Score = 179 bits (455), Expect = 9e-50 Identities = 117/364 (32%), Positives = 185/364 (50%), Gaps = 13/364 (3%) Query: 13 AAMAIAGFASYSMAAD-TIKIALAGPVTGPVAQYGDMQRAGALMAIEQIN-KAGGVNGAQ 70 AA+ +AG A ++ A + IKI +GP++GP A G G +A+E++N K V G Sbjct: 17 AALLLAGHAPHASAQEQVIKIGHSGPLSGPNAFAGKDNENGVRLAVEELNAKKIVVEGKA 76 Query: 71 L--EGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEGVLMITPSA 128 L E V DD CD + V+VA K+V+ GVKFV+G CS PA+ +Y D G M++ Sbjct: 77 LKFELVSEDDQCDARTGVSVAQKLVDSGVKFVMGPYCSGVAIPASRVYNDGGA-MVSTVG 135 Query: 129 TAPEITSRGYKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGEGIATEVKKT 188 T P++T GYK +FR I D G + A+ K K +AV+ D+ +G+G+A + K Sbjct: 136 TNPKVTEGGYKNLFRIIASDTQIGSNMAVYAAQVLKVKQVAVIDDRTAFGQGVAEQFTKE 195 Query: 189 VEDAGIKVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLRQAKQAGLDAR 248 + G+ V E DF ++++ LK Q ++FGGY P+ + RQ KQ GL A+ Sbjct: 196 AKKQGLTVVGQEFTTDKATDFLSILTSLKAKQPQAIFFGGYAPQAAPMARQMKQLGLTAK 255 Query: 249 FMGPEGVGNSEITAIAGDASEGML-----ATLPRAFEQDPKNKALIDAFKAKNQDPSGIF 303 +G + + + E+ + GDA + T+ P KA +KA+ + + + Sbjct: 256 LLGGDTLCSPEVGKLGGDAVNDTVFCAQGGTMLDKVANGPAFKA---KYKARFKLDADAY 312 Query: 304 VLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDFTVYEW 363 Y V +A ++KA P KV + ++ + G +D+KG+LK TV + Sbjct: 313 AASYYDQVMFMANAMQKANSTQPAKVGAQMLQSSHQGVAGTYAYDDKGNLKQAPITVLTF 372 Query: 364 HKDA 367 A Sbjct: 373 RNAA 376 Lambda K H 0.316 0.133 0.377 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: 368 Number of extensions: 19 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: 373 Length of database: 383 Length adjustment: 30 Effective length of query: 343 Effective length of database: 353 Effective search space: 121079 Effective search space used: 121079 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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