GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluP in Shewanella amazonensis SB2B

Align D-mannitol and D-mannose transporter (MFS superfamily) (characterized)
to candidate 6936095 Sama_0292 glucose/galactose transporter (RefSeq)

Query= reanno::SB2B:6936374
         (413 letters)



>FitnessBrowser__SB2B:6936095
          Length = 389

 Score =  520 bits (1340), Expect = e-152
 Identities = 266/373 (71%), Positives = 304/373 (81%), Gaps = 1/373 (0%)

Query: 28  MTSLFFIWGFITALNDILIPHLKGIFDLSYTQAMLVQFCFFGAYFLVSPLAGVLIARIGY 87
           MT+LFFIWGFITALNDILIPHLK  F+LSYTQAMLVQFCFFGAYF+VSP AG LI +IGY
Sbjct: 1   MTTLFFIWGFITALNDILIPHLKAAFELSYTQAMLVQFCFFGAYFIVSPFAGKLIEKIGY 60

Query: 88  LRGIIFGLSTMATGCLLFYPASSLEQYALFLLALFVLASGITILQVSANPFVARLGPERT 147
           +RGI+ GL TMATGCLLFYPA+ +  YALFLL LFVLASGITILQVSANP+VA LG ERT
Sbjct: 61  IRGIVTGLCTMATGCLLFYPAAEVSVYALFLLGLFVLASGITILQVSANPYVAILGAERT 120

Query: 148 AASRLNLAQALNSLGHTLGPLFGSLLIFGAAAGTHEAVQLPYLLLAAVIGIIAVGFIFLG 207
           AASRL+LAQA+NSLGHTL PLFG+ LIFGAA+  H AVQLPYL+LA  + + AVGF+FL 
Sbjct: 121 AASRLSLAQAINSLGHTLAPLFGAALIFGAASNAH-AVQLPYLILAGAVLLTAVGFVFLK 179

Query: 208 GKVKHADMGVDHRHKGSLLSHKRLLLGALAIFLYVGAEVSIGSFLVNYFAEPSIGGLDEK 267
                 D      H  S+  HK L+LGALAIFLYVGAEVS+GSFLVNYF+E  I  L E+
Sbjct: 180 LPTLQTDHETQVSHSDSIWQHKHLVLGALAIFLYVGAEVSVGSFLVNYFSESHIAALSEQ 239

Query: 268 SAAELVSWYWGGAMIGRFAGAALTRRFNPAMVLAANAVFANLLLMLTIVSSGELALVAVL 327
            A+ +VS+YWGGAM+GRF G+ALTR   P  VLA NA+ A LLL+LT+ SSG LA+ +VL
Sbjct: 240 EASRMVSYYWGGAMVGRFVGSALTRILQPTYVLATNALMAILLLVLTMNSSGALAMWSVL 299

Query: 328 AVGFFNSIMFPTIFTLAIEGLGELTSRGSGLLCQAIVGGALLPVIQGVVADNVGVQLSFI 387
           AVGFFNSIMFPTIFTLAI GLG LTSRGSGLLCQAIVGGA+LP++QGVVAD+  VQ SF+
Sbjct: 300 AVGFFNSIMFPTIFTLAIRGLGPLTSRGSGLLCQAIVGGAILPLLQGVVADSSSVQFSFV 359

Query: 388 VPTFCYFYICWYA 400
           +P   Y YI WYA
Sbjct: 360 IPMVAYLYIGWYA 372


Lambda     K      H
   0.329    0.142    0.425 

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: 517
Number of extensions: 16
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: 413
Length of database: 389
Length adjustment: 31
Effective length of query: 382
Effective length of database: 358
Effective search space:   136756
Effective search space used:   136756
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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