GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Erythrobacter gangjinensis K7-2

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate WP_047007739.1 AAW01_RS12210 ABC transporter ATP-binding protein

Query= BRENDA::Q97UY8
         (353 letters)



>NCBI__GCF_001010925.1:WP_047007739.1
          Length = 239

 Score =  128 bits (322), Expect = 1e-34
 Identities = 81/229 (35%), Positives = 128/229 (55%), Gaps = 6/229 (2%)

Query: 4   IIVKNVSKVFKKGK--VVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGE 61
           I V+ +++ F+ G+  +  L  ++ +I  GE   ++G SG+GKTT + I+ G+  P+ GE
Sbjct: 11  ISVRGITRDFEAGQQTITVLHGIDTDIRAGELTYVVGESGSGKTTLISIMCGILWPTEGE 70

Query: 62  LY-FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120
           +  F   + + +   +V      IG +FQ + L P++ A  N + PL    M ++E R+R
Sbjct: 71  VQVFGTDIYSLSDTDLVEFRLNNIGFIFQQYNLIPSIDAASNASVPLIAQGMDRDEARER 130

Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180
              +   L+I       P +LSGGQQQRVA+ARALV +P L++ DEP + LDA       
Sbjct: 131 AVAIMDKLNIRDQAGKLPSQLSGGQQQRVAIARALVHEPRLVVCDEPTAALDASSGRRVM 190

Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGK--PED 227
            L++EV        ++V+HD   +F +ADR+ VL  GK+   GK  PED
Sbjct: 191 DLLREVAVAEDRACIIVTHDNR-VFDLADRILVLEDGKITHDGKEMPED 238


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: 202
Number of extensions: 11
Number of successful extensions: 2
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: 239
Length adjustment: 26
Effective length of query: 327
Effective length of database: 213
Effective search space:    69651
Effective search space used:    69651
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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