GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Shewanella loihica PV-4

Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)

Query= reanno::acidovorax_3H11:Ac3H11_791
         (363 letters)



>FitnessBrowser__PV4:5207560
          Length = 369

 Score =  116 bits (290), Expect = 1e-30
 Identities = 80/238 (33%), Positives = 120/238 (50%), Gaps = 8/238 (3%)

Query: 20  DMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTV------DGKDVTGMPVRD 73
           D     ++G V  ++G +  GK++LMR++AGL  P +G +          +    +  + 
Sbjct: 21  DAEFVCKAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSSESGRYLTPQQ 80

Query: 74  RNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDARVREIASRLHIDMFLDRYPAELSG 133
           R++  V Q F  +P+M   AN+ + L    +    AR ++   R+++    DR PA LSG
Sbjct: 81  RHLGYVPQHFGLFPNMTALANVVAALDHIPKAERVARAKDWLERVNLHGLPDRLPANLSG 140

Query: 134 GQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQSTVVYATTEPGE 193
           GQ+QRVALARALA+   ++LLDEP   +D + RE L  EL +L       V+  T +  E
Sbjct: 141 GQRQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLAIPVIMVTHDLNE 200

Query: 194 ALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAASATAQGVRLQ 251
           ALLL     ++ +G LLQ G   EV   P +  VA+       NL  A   AQ    Q
Sbjct: 201 ALLLADRMILISQGTLLQQGSPREVLSRPRNEAVAKQMG--LRNLFDAHVVAQEAERQ 256


Lambda     K      H
   0.318    0.133    0.375 

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: 220
Number of extensions: 7
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: 363
Length of database: 369
Length adjustment: 30
Effective length of query: 333
Effective length of database: 339
Effective search space:   112887
Effective search space used:   112887
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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