GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Shewanella sp. ANA-3

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__ANA3:7026050
          Length = 376

 Score =  189 bits (479), Expect = 1e-52
 Identities = 102/249 (40%), Positives = 154/249 (61%), Gaps = 11/249 (4%)

Query: 4   IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63
           I + N+SK F  G+  AL  +N++I+ GE  G+LGPSG+GKTT +RIIAGL+   +G+++
Sbjct: 3   IRLTNISKKF--GQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60

Query: 64  FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLT----NMKMSKEEIRK 119
           F +R V       V   DR++G VFQ +AL+ ++T  +N+AF L       + SK EI+K
Sbjct: 61  FGNRDVTQ-----VHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQK 115

Query: 120 RVEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSA 179
           RV  + +++ + H+   +P +LSGGQ+QR+ALARAL   P +LLLDEPF  LDA++R   
Sbjct: 116 RVSHLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKEL 175

Query: 180 RALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVAS 239
           R  ++ +   L  T + V+HD  +   ++DRV V+  G + QV  P +LY  P S  V  
Sbjct: 176 RRWLRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFD 235

Query: 240 LIGEINELE 248
            +G +N  E
Sbjct: 236 FLGNVNRFE 244


Lambda     K      H
   0.319    0.139    0.390 

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: 324
Number of extensions: 16
Number of successful extensions: 3
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: 353
Length of database: 376
Length adjustment: 29
Effective length of query: 324
Effective length of database: 347
Effective search space:   112428
Effective search space used:   112428
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: 49 (23.5 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