Align High-affinity branched-chain amino acid transport ATP-binding protein LivG aka B3455, component of Leucine; leucine/isoleucine/valine porter (characterized)
to candidate WP_017368436.1 BA79_RS17265 ABC transporter ATP-binding protein
Query= TCDB::P0A9S7 (255 letters) >NCBI__GCF_000691145.1:WP_017368436.1 Length = 571 Score = 105 bits (261), Expect = 3e-27 Identities = 70/222 (31%), Positives = 114/222 (51%), Gaps = 18/222 (8%) Query: 21 VNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPTGGTILLRDQHLEG-LPGQQIAR 79 +NN++ + E++S+ G NGAGKTT+ L F KPT GTI L + G Q+ R Sbjct: 319 LNNISFTVKKGEMISIAGANGAGKTTLSKVLCAFEKPTKGTIHLNGDDITGDTIKQRSER 378 Query: 80 MGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGLLKTPSFRRAQSEALDRAATWLE 139 +GVV + + ++M E L + +K + + DR L+ Sbjct: 379 IGVVMQNPNQMISKQMIFDEVALGLVLRGVK----------------EDDIKDRVERVLK 422 Query: 140 RIGLLEHANRQASNLAYGDQRRLEIARCMVTQPEILMLDEPAAGLNPKETKELDELIAEL 199 GL N S L++G ++R+ IA +V +PEI++LDEP AG + + E+ + +L Sbjct: 423 VCGLYPFRNWPISALSFGQKKRVTIASILVLEPEIIILDEPTAGQDFRHYTEMMTFLEQL 482 Query: 200 RNHHNTTILLIEHDMKLVMGISDRIYVVNQGTPLANGTPEQI 241 N TIL+I HDM L++ + R V++ G +A+ TP ++ Sbjct: 483 -NQQGVTILMITHDMHLMLEYTTRTIVISDGEKIADDTPAKV 523 Score = 81.6 bits (200), Expect = 3e-20 Identities = 72/267 (26%), Positives = 123/267 (46%), Gaps = 33/267 (12%) Query: 1 MSQPLLSVN--GLMMRFGGLLAVNNVNLELYPQEIVSLIGPNGAGKTTVFNCLTGFYKPT 58 M +P++ G R + +VNL +Y E V + GP+G+GK+T+ +C+ G + Sbjct: 1 MKKPMIQFEHFGFKYRSQAEPTLKDVNLTIYEGEKVLIAGPSGSGKSTLAHCINGLVPAS 60 Query: 59 GGTILLRDQHLEGLPGQQIARMGVVRTFQHVRLFREMTVIENLLVAQHQQLKTGLFSGL- 117 + H+ G + +E + LV Q G F GL Sbjct: 61 YKGSMEGSLHIGGKNAE-----------------KENIFSLSQLVGTVLQDPDGQFIGLT 103 Query: 118 --------LKTPSFRRAQSEA-LDRAATWLERIGLLEHANRQASNLAYGDQRRLEIARCM 168 L+ R + + +++AA E G L + + S G ++R+ IA + Sbjct: 104 VGEDIAFTLENDQVTREEMKTRVEKAAKLTEVDGKLASSVHELSG---GQKQRVAIAGVL 160 Query: 169 VTQPEILMLDEPAAGLNPKETKELDELIAELRNHHNTTILLIEHDMK-LVMGISDRIYVV 227 V +IL+ DEP A L+P KE+ +LI L+ T++++EH ++ ++ DRI VV Sbjct: 161 VNDVDILLFDEPLASLDPATGKEVIDLIDRLQKETKKTVVMVEHRLEDVLFRHVDRIIVV 220 Query: 228 NQGTPLANGTPEQIRNNPDVIRAYLGE 254 N GT A+ TP+++ + + AYL E Sbjct: 221 NDGTIAADMTPDELLASNVLEAAYLRE 247 Lambda K H 0.320 0.137 0.395 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: 367 Number of extensions: 18 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 255 Length of database: 571 Length adjustment: 30 Effective length of query: 225 Effective length of database: 541 Effective search space: 121725 Effective search space used: 121725 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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