GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Desulfovibrio vulgaris Miyazaki F

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate 8500738 DvMF_1481 ABC transporter related (RefSeq)

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__Miya:8500738
          Length = 259

 Score =  191 bits (485), Expect = 1e-53
 Identities = 100/249 (40%), Positives = 152/249 (61%)

Query: 17  SLLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVL 76
           +LL  + LS +FGG+RA+D A    + G+IT LIGPNGAGKTTL N ++  +RPD G V 
Sbjct: 2   TLLAVRDLSVAFGGIRALDAASFTAQAGAITALIGPNGAGKTTLVNCVTGMVRPDSGNVA 61

Query: 77  FNGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRV 136
           F+G  I  +A H++   G  RTFQ  +V   +++LEN+++          L  ++    V
Sbjct: 62  FDGRDITGMAAHRLPRLGLARTFQHLRVFGSMSLLENVMVGLHGHVRTGMLSSMLRLPGV 121

Query: 137 QKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAG 196
           ++ ERA R+ AM  L+  GL  +A   AG L  G +K L +ARAL+ +P++ILLDEP AG
Sbjct: 122 RRTERAMRDAAMRALDFTGLADRADGAAGLLPYGDQKRLVLARALVGDPRMILLDEPVAG 181

Query: 197 VNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSD 256
           +NP    ++   I+    +G+  L+IEH+M ++M +   V VL  G  +A+G P +++ +
Sbjct: 182 LNPAETHEMGGLILALRARGVAVLLIEHDMSLVMRVSDAVVVLCSGAKIAEGAPGEVKRN 241

Query: 257 PRVLEAYLG 265
           P V+ AYLG
Sbjct: 242 PEVVNAYLG 250


Lambda     K      H
   0.319    0.136    0.389 

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: 201
Number of extensions: 10
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: 267
Length of database: 259
Length adjustment: 25
Effective length of query: 242
Effective length of database: 234
Effective search space:    56628
Effective search space used:    56628
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 (21.7 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