GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Desulfovibrio vulgaris Miyazaki F

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 8500738 DvMF_1481 ABC transporter related (RefSeq)

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Miya:8500738
          Length = 259

 Score =  211 bits (536), Expect = 2e-59
 Identities = 120/263 (45%), Positives = 165/263 (62%), Gaps = 10/263 (3%)

Query: 13  TLLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMIT 72
           TLL V  LS+ FGG+ A++  SF A+ G ITALIGPNGAGKTT+ NC+TG  +P  G + 
Sbjct: 2   TLLAVRDLSVAFGGIRALDAASFTAQAGAITALIGPNGAGKTTLVNCVTGMVRPDSGNVA 61

Query: 73  FNQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTI 132
           F+ +        RLP         +ARTFQ++R+F  +++LEN++V  H  +      ++
Sbjct: 62  FDGRDITGMAAHRLP------RLGLARTFQHLRVFGSMSLLENVMVGLHGHVRTGMLSSM 115

Query: 133 LGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192
           L L GV   +R   +A   A   L+   L DRAD  AG LPYG Q+RL +ARA+   P +
Sbjct: 116 LRLPGVRRTERAMRDAAMRA---LDFTGLADRADGAAGLLPYGDQKRLVLARALVGDPRM 172

Query: 193 LCLDEPAAGLNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKIS 252
           + LDEP AGLNP E+  +  L+ ++RA  G ++LLIEHDMS+VM +SD VVVL  G KI+
Sbjct: 173 ILLDEPVAGLNPAETHEMGGLILALRAR-GVAVLLIEHDMSLVMRVSDAVVVLCSGAKIA 231

Query: 253 DGTPDHVKNDPRVIAAYLGVEDE 275
           +G P  VK +P V+ AYLG  +E
Sbjct: 232 EGAPGEVKRNPEVVNAYLGGGEE 254


Lambda     K      H
   0.318    0.136    0.386 

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: 211
Number of extensions: 19
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: 292
Length of database: 259
Length adjustment: 25
Effective length of query: 267
Effective length of database: 234
Effective search space:    62478
Effective search space used:    62478
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 (21.7 bits)
S2: 47 (22.7 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