GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Shewanella sp. ANA-3

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__ANA3:7026373
          Length = 349

 Score =  187 bits (475), Expect = 4e-52
 Identities = 106/272 (38%), Positives = 163/272 (59%), Gaps = 9/272 (3%)

Query: 21  LDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLIVPPE 80
           L  +++ +  GE   +LGPSG GKTT +R +AGL   S GE+  + + V+  G+  VP E
Sbjct: 20  LKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQINGKTVSGAGQF-VPSE 78

Query: 81  DRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLNHFPRE 140
            R IGM+FQ +AL+P+LT  ENI F +   K++  + + R++++  ++ +  +   +P E
Sbjct: 79  QRGIGMIFQDYALFPHLTVAENILFGVA--KLTPAQRKARLDDMLALVKLEGLAKRYPHE 136

Query: 141 LSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVSHD 200
           LSGGQQQRV++ARAL  +P LLLLDEPFSN+DA++R S  A ++ +  +  V+ + V+H 
Sbjct: 137 LSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSILKQRNVSAVFVTHS 196

Query: 201 PADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKVTNEGVV--- 257
             + F  AD + +  +G +VQ G+ E+LY  P S  VA  +G  N L  +V +   V   
Sbjct: 197 KDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLGSGNYLPAEVIDGHSVVTP 256

Query: 258 IGSLRFPVSVSSDRAIIG---IRPEDVKLSKD 286
           IG LR    +S   A  G   +RP+ + LS D
Sbjct: 257 IGELRSLTPLSQSHAFNGQVFLRPQQLALSAD 288


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: 255
Number of extensions: 8
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: 349
Length adjustment: 29
Effective length of query: 324
Effective length of database: 320
Effective search space:   103680
Effective search space used:   103680
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