Align ABC-type branched-chain amino acid transport system, periplasmic component 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:D8IUY1 (378 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4169 Length = 383 Score = 427 bits (1098), Expect = e-124 Identities = 206/377 (54%), Positives = 279/377 (74%), Gaps = 1/377 (0%) Query: 2 FKRVSGLNIIAASLALIPAFAMAQETQVVKIGFSSPLTGPQASAGKDNQGGLMMAIERLN 61 F+ ++ I A LA A AQE QV+KIG S PL+GP A AGKDN+ G+ +A+E LN Sbjct: 8 FRTLTPAAIAALLLAGHAPHASAQE-QVIKIGHSGPLSGPNAFAGKDNENGVRLAVEELN 66 Query: 62 AQPITVGGKKIKFDVIAEDDQADPKSGVAVAQKLADQGVKAIVGPYNSGVTIPASRVYND 121 A+ I V GK +KF++++EDDQ D ++GV+VAQKL D GVK ++GPY SGV IPASRVYND Sbjct: 67 AKKIVVEGKALKFELVSEDDQCDARTGVSVAQKLVDSGVKFVMGPYCSGVAIPASRVYND 126 Query: 122 AGIVVATVASNPKITQQGFATLFRVAASDSQLGGKMALYAAKELKFKRVAVIDDRTAYGQ 181 G +V+TV +NPK+T+ G+ LFR+ ASD+Q+G MA+YAA+ LK K+VAVIDDRTA+GQ Sbjct: 127 GGAMVSTVGTNPKVTEGGYKNLFRIIASDTQIGSNMAVYAAQVLKVKQVAVIDDRTAFGQ 186 Query: 182 GLAQEFIKVAKANGIDVVSTDFTNDKATDFTAILTSIKGKKPDAVFLGGYAPQGGPIKRQ 241 G+A++F K AK G+ VV +FT DKATDF +ILTS+K K+P A+F GGYAPQ P+ RQ Sbjct: 187 GVAEQFTKEAKKQGLTVVGQEFTTDKATDFLSILTSLKAKQPQAIFFGGYAPQAAPMARQ 246 Query: 242 MKQLGVDVPLMGGDGICSPEMGRLGGDAIGESVYCTQGGTMLDKAKEGKVFSDEYQKKYN 301 MKQLG+ L+GGD +CSPE+G+LGGDA+ ++V+C QGGTMLDK G F +Y+ ++ Sbjct: 247 MKQLGLTAKLLGGDTLCSPEVGKLGGDAVNDTVFCAQGGTMLDKVANGPAFKAKYKARFK 306 Query: 302 RPAETYAVSFYDGMMLIAQAMKQANSVDPKQFGPALAKISYKGVAGQYDFDANHDLKQSP 361 A+ YA S+YD +M +A AM++ANS P + G + + S++GVAG Y +D +LKQ+P Sbjct: 307 LDADAYAASYYDQVMFMANAMQKANSTQPAKVGAQMLQSSHQGVAGTYAYDDKGNLKQAP 366 Query: 362 VTVYRFKDGLPVPLTSY 378 +TV F++ PVPL SY Sbjct: 367 ITVLTFRNAAPVPLASY 383 Lambda K H 0.316 0.134 0.378 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: 500 Number of extensions: 18 Number of successful extensions: 1 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: 378 Length of database: 383 Length adjustment: 30 Effective length of query: 348 Effective length of database: 353 Effective search space: 122844 Effective search space used: 122844 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