Align Branched chain amino acid ABC transporter substrate-binding protein (characterized, see rationale)
to candidate Ac3H11_4169 Branched-chain amino acid ABC transporter, amino acid-binding protein (TC 3.A.1.4.1)
Query= uniprot:A0A165KTD4 (375 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4169 Length = 383 Score = 343 bits (879), Expect = 6e-99 Identities = 177/363 (48%), Positives = 239/363 (65%), Gaps = 3/363 (0%) Query: 13 IAAAAGVASAQEQVVKIGHVAPVSGAQAHYGKDNENGARMAIEELNAQGVTIGGKKIKFE 72 +A A ASAQEQV+KIGH P+SG A GKDNENG R+A+EELNA+ + + GK +KFE Sbjct: 21 LAGHAPHASAQEQVIKIGHSGPLSGPNAFAGKDNENGVRLAVEELNAKKIVVEGKALKFE 80 Query: 73 LVAEDDAADPKQGTAAAQKLCDAKVAGVVGHLNSGTTIPASKVYNDCGIPHVTGAATNPN 132 LV+EDD D + G + AQKL D+ V V+G SG IPAS+VYND G V+ TNP Sbjct: 81 LVSEDDQCDARTGVSVAQKLVDSGVKFVMGPYCSGVAIPASRVYNDGGAM-VSTVGTNPK 139 Query: 133 LTKPGYKTTFRIIANDNALGAGLAFYAVDTLKLKTVAIIDDRTAYGQGVADVFKKTATAK 192 +T+ GYK FRIIA+D +G+ +A YA LK+K VA+IDDRTA+GQGVA+ F K A + Sbjct: 140 VTEGGYKNLFRIIASDTQIGSNMAVYAAQVLKVKQVAVIDDRTAFGQGVAEQFTKEAKKQ 199 Query: 193 GMKVVDEQFTTDKATDFMAILTAIKAKNPDAIFYGGMDPQGGPMLRQMEQLGMGNVKYFG 252 G+ VV ++FTTDKATDF++ILT++KAK P AIF+GG PQ PM RQM+QLG+ K G Sbjct: 200 GLTVVGQEFTTDKATDFLSILTSLKAKQPQAIFFGGYAPQAAPMARQMKQLGL-TAKLLG 258 Query: 253 GDGICTSEIAKLAAGAKTLGNVICAEGGSSLAKMPGGTAWKAKYDAKYPNQFQVYSPYTY 312 GD +C+ E+ KL A V CA+GG+ L K+ G A+KAKY A++ Y+ Y Sbjct: 259 GDTLCSPEVGKLGGDAVN-DTVFCAQGGTMLDKVANGPAFKAKYKARFKLDADAYAASYY 317 Query: 313 DATFLIVDAMKRANSVDPKVYTPELAKSSFKGVTSTIAFEPNGEMKNPAITLYVYKDGKK 372 D + +AM++ANS P ++ +SS +GV T A++ G +K IT+ +++ Sbjct: 318 DQVMFMANAMQKANSTQPAKVGAQMLQSSHQGVAGTYAYDDKGNLKQAPITVLTFRNAAP 377 Query: 373 TPL 375 PL Sbjct: 378 VPL 380 Lambda K H 0.315 0.131 0.375 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: 433 Number of extensions: 18 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: 375 Length of database: 383 Length adjustment: 30 Effective length of query: 345 Effective length of database: 353 Effective search space: 121785 Effective search space used: 121785 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: 42 (22.0 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