GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG in Bacillus altitudinis 41KF2b

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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