GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bztC in Desulfovibrio vulgaris Hildenborough

Align BztC, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= TCDB::Q52665
         (434 letters)



>MicrobesOnline__882:206177
          Length = 596

 Score =  129 bits (325), Expect = 2e-34
 Identities = 91/252 (36%), Positives = 139/252 (55%), Gaps = 19/252 (7%)

Query: 187 GIGLVVAALFWLYAAAPIEAALQSALPLALPEVDSDQF----GGFLLALVIGVTAIVVSL 242
           G+  V A   + +    I   L++ L    P   SD+     GG   +L++ V AI VS 
Sbjct: 346 GLLFVTARGLYNFNWGVIADNLRTLLIWHFPNGQSDELFMGLGGLAYSLLMAVIAISVSF 405

Query: 243 PLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLLLQYFLPP--GTNFDLIL 300
            +G+++ +GR SD  I +   +  IE +RG PLI ++F     + +F+P    T F++  
Sbjct: 406 FIGLVVGIGRTSDNRICRIPCLLYIELIRGNPLIIVIFW----IYFFIPVLFNTFFNVFW 461

Query: 301 RVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGLDYWQAQRLIIMPQALKISIPGI 360
              I +TLF  AY+AE++R G+  +P GQ EAA + GL + Q  R II+PQALK  IP I
Sbjct: 462 SATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTMRRIILPQALKQMIPAI 521

Query: 361 VSSFIGLFKDTTLVAFVGLFD---PLKGISNVVRSDMAWKGTYWEPYIFVALIFFLFNFS 417
           V  FI +FKDT+L   +G+ +     +GI+N +   M +     E Y  VA ++F+  +S
Sbjct: 522 VGQFIAIFKDTSLAFVLGVLELTFVAQGINNRL---MVYP---MEIYGTVAFLYFICCWS 575

Query: 418 MSRYSMYLERKL 429
           MS Y+  LER+L
Sbjct: 576 MSVYAARLERRL 587



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 50/161 (31%), Positives = 85/161 (52%), Gaps = 8/161 (4%)

Query: 226 GFLLALVIGVTAIVVSLPLGILLALGRQSDMLIVKSLSVGIIEFVRGVPLITLLFTASLL 285
           G  + + I + +  ++L LG +L + R S    ++  +  ++EF R  PL+  LF     
Sbjct: 60  GLGVTVRISLISSALALGLGTVLGIARLSLFAPLRLTATAVVEFFRNTPLLVQLFFWYFA 119

Query: 286 LQYFLPPGT-------NFDLILRVVILVTLFAAAYIAEVIRGGLAALPRGQYEAADALGL 338
               LP          NF+     + L +++ +A++AEVIR GL ++P+G  EAA + GL
Sbjct: 120 FPAILPENIRELLFTGNFEFWCATIGL-SVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGL 178

Query: 339 DYWQAQRLIIMPQALKISIPGIVSSFIGLFKDTTLVAFVGL 379
           +Y Q  R II+P A +  IP + S F+   K+++L   VG+
Sbjct: 179 NYVQVLRTIILPMAFRAIIPPLGSEFLNNMKNSSLAMVVGV 219


Lambda     K      H
   0.329    0.143    0.457 

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: 744
Number of extensions: 51
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: 2
Length of query: 434
Length of database: 596
Length adjustment: 34
Effective length of query: 400
Effective length of database: 562
Effective search space:   224800
Effective search space used:   224800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 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