GapMind for catabolism of small carbon sources

 

Aligments for a candidate for malF in Synechococcus elongatus PCC 7942

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter

Query= reanno::Koxy:BWI76_RS01825
         (514 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0949 Synpcc7942_0949 permease
           protein of sugar ABC transporter
          Length = 292

 Score =  110 bits (274), Expect = 9e-29
 Identities = 82/258 (31%), Positives = 127/258 (49%), Gaps = 20/258 (7%)

Query: 257 VTIGWDNFTRVFQDEGIQKPFFAIFVWTVVFSVLTVILTVAVGMVLACLVQWEALKGKAI 316
           V IG  N+ R++ D       F     T VF+V +V L + +G+ +A L+  +  + +  
Sbjct: 44  VFIGLANYQRLWGDSRFWGDLFN----TTVFTVTSVSLELVLGLAIALLLH-QPSRWRGP 98

Query: 317 YRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGIKPA--WFSDPTTARTMIII 374
            R + +LP+ +P+ +  L +  +FN  +G  N  L  L  I     W  +P  A   ++ 
Sbjct: 99  LRTIALLPWVLPTAVMALGWAWIFNDPYGVWNDWLQQLGWIAAPINWLGNPRWAWLTLVA 158

Query: 375 VNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGATPFQNFFKITLPLLIKPLTPLMIASF 434
            + W   P++ IL +   +AIP+DLYEA  ++GAT +Q+F++ITLPLL   L   ++   
Sbjct: 159 ADVWKTTPFVAILLLAGRQAIPEDLYEAHCLEGATAWQSFWQITLPLLRPQLAIALLFRS 218

Query: 435 AFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVSYTYRIAFEGGGGQDFGLAA--AIAT 492
           A  F  F L++++T GG        PA  T+ L  Y Y  A       DFG  A  AI T
Sbjct: 219 AQAFGLFDLVKVMTGGG--------PANSTETLALYAYTTALR---YLDFGYGATLAIVT 267

Query: 493 LIFLLVGLLAIVNLKATR 510
              L  GL  I  L  +R
Sbjct: 268 AAILAAGLGLIWGLGRSR 285


Lambda     K      H
   0.325    0.140    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: 415
Number of extensions: 21
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: 514
Length of database: 292
Length adjustment: 30
Effective length of query: 484
Effective length of database: 262
Effective search space:   126808
Effective search space used:   126808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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