GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Phaeobacter inhibens BS107

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate GFF3638 PGA1_262p00420 Transcriptional regulator/sugar kinase

Query= BRENDA::P0A4E1
         (317 letters)



>FitnessBrowser__Phaeo:GFF3638
          Length = 404

 Score =  142 bits (358), Expect = 1e-38
 Identities = 95/315 (30%), Positives = 157/315 (49%), Gaps = 24/315 (7%)

Query: 6   GVDIGGTKIAAGVVDEEGNILSTHKVPT---PTTPEAIVDAIASAVE-----GARVGHEI 57
           G+ +    I   + D EG  L +H++P      +PE++ + I  A++     G     +I
Sbjct: 91  GLKLSHHAITTLITDFEGTELISHEMPLRGGQMSPESLCEKIVEALDQSCAKGGLTRTQI 150

Query: 58  VAVGIGAAGYVNRQRSTVYFAPNIDWRQEPLKEKVEARVGLPVVVENDANAAAWGEYKFG 117
             VGIG AG ++ +R+ +Y++ +++ R   L   +++ + +PV ++NDAN  A  E+ FG
Sbjct: 151 SGVGIGMAGVMDAERNFIYWSSSLNVRNIDLGSALKSHLSMPVFIDNDANLVAKAEHLFG 210

Query: 118 GGKGHRNVICITLGTGLGGGIIIGNKLRRGHFGVAAEFGHIRMVPDGLLCGCGSQGCWEQ 177
            G    N + +T+  G+G GI+I N++ RG  G  AEFGHI++  +G LC CG +GC E 
Sbjct: 211 EGDTRSNFVVVTVEHGVGMGIVIDNQIYRGARGCGAEFGHIKVQLEGALCQCGQRGCLEA 270

Query: 178 YASGRALVRYAKQRANATPERAEVLLALGDGTPDGIEGKHISVAARQGCPVAVDSYRELA 237
           Y    AL+R A   +    ER + L +L               A  +G  +A        
Sbjct: 271 YVGDYALLREANITSGV--ERHKDLASL-------------YAAVAEGDMMAQSILDRAG 315

Query: 238 RWAGAGLADLASLFDPSAFIVGGGLSDEGDLVLDPIRKSYKRWLVGGNWRPVADVIAAQL 297
           R    GLA++ ++FDP   ++ G     G L  D + +  +RW+V  +  P+ +V     
Sbjct: 316 RMFAMGLANIVNIFDPQMIVLAGAQLAFGYLSSDKVVEEMRRWVVQVD-GPLPEVRVHGW 374

Query: 298 GNKAGLVGAADLARE 312
           GN+    GAA  A E
Sbjct: 375 GNQMWAKGAAAYAIE 389


Lambda     K      H
   0.318    0.139    0.426 

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: 308
Number of extensions: 19
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: 317
Length of database: 404
Length adjustment: 29
Effective length of query: 288
Effective length of database: 375
Effective search space:   108000
Effective search space used:   108000
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: 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