GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SynE:Synpcc7942_0949
          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:

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