GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Phaeobacter inhibens BS107

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__Phaeo:GFF262
          Length = 348

 Score =  225 bits (574), Expect = 1e-63
 Identities = 127/292 (43%), Positives = 191/292 (65%), Gaps = 19/292 (6%)

Query: 1   MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60
           M ++ + +V KV+  G V A+ + +  IE+GE   ++GPSG GK+T +R+IAGL+  + G
Sbjct: 1   MAQVTLNSVRKVYPNG-VEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEG 59

Query: 61  ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
            L   DR+V +     V P DR I MVFQ +ALYP++T  +NIA+ L N K  + EI+++
Sbjct: 60  TLEIGDRVVNN-----VDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQK 114

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
           V E AK+L++   L+  P +LSGGQ+QRVA+ RA+V+DP+L L DEP SNLDA++R+  R
Sbjct: 115 VAEAAKMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMR 174

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240
             +K +Q RLGVT + V+HD  +   +ADR+ VL  G++ Q+G P ++Y NP S+ VAS 
Sbjct: 175 IEIKALQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASF 234

Query: 241 IG--EINELEGKVTN------EGVVIGSLRFPVSVSSDRAI-IGIRPEDVKL 283
           +G   +N L+  + N      +GV +G+L      S+  A+ +GIRPEDV+L
Sbjct: 235 MGAPPMNLLDATIANGQVTLPDGVSMGAL----DTSAQGAVKLGIRPEDVQL 282


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: 313
Number of extensions: 17
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: 348
Length adjustment: 29
Effective length of query: 324
Effective length of database: 319
Effective search space:   103356
Effective search space used:   103356
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