GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcV in Shewanella amazonensis SB2B

Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate 6936480 Sama_0668 iron(III) ABC transporter, ATP-binding protein (RefSeq)

Query= BRENDA::Q97UY8
         (353 letters)



>FitnessBrowser__SB2B:6936480
          Length = 341

 Score =  176 bits (445), Expect = 1e-48
 Identities = 102/266 (38%), Positives = 160/266 (60%), Gaps = 9/266 (3%)

Query: 21  LDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELYFDDRLVASNGKLIVPPE 80
           L  +N+ +  GE   +LGPSG GKTT +R IAGL   S G +  + + V+++G   V PE
Sbjct: 19  LRGLNLTLTQGEITALLGPSGCGKTTLLRTIAGLQDISAGSIAINGKTVSADG-CFVAPE 77

Query: 81  DRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEEVAKILDIHHVLNHFPRE 140
            R IGM+FQ +AL+P+LT  +NI F +   ++ K+    R+EE+  ++ +  +   +P E
Sbjct: 78  KRSIGMIFQDYALFPHLTVADNILFGVR--QLDKQSRSVRLEEMLSLVKLEGLGKRYPHE 135

Query: 141 LSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALVKEVQSRLGVTLLVVSHD 200
           LSGGQQQRV++ARAL  +P LLLLDEPFSN+DA++R +    ++ +     V+ + V+H 
Sbjct: 136 LSGGQQQRVSIARALAYEPDLLLLDEPFSNIDAQVRRALMLEIRAILKARNVSAVFVTHS 195

Query: 201 PADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGEINELEGKVTNEGVVIGS 260
             + FA AD + +   G++VQ G PE LY +P +  VA  +G  N L+ ++   G +I +
Sbjct: 196 KDEAFAFADTLALFEAGRIVQHGIPETLYQSPNTPYVADFLGASNYLDVRL-EAGQLIST 254

Query: 261 L-RFPV----SVSSDRAIIGIRPEDV 281
           L  FP+      +S+     +RPE +
Sbjct: 255 LGAFPLPQDFKAASETGRWLLRPEQL 280


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: 269
Number of extensions: 15
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: 341
Length adjustment: 29
Effective length of query: 324
Effective length of database: 312
Effective search space:   101088
Effective search space used:   101088
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