GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Echinicola vietnamensis KMM 6221, DSM 17526

Align ATPase (characterized, see rationale)
to candidate Echvi_3653 Echvi_3653 ABC-type sulfate/molybdate transport systems, ATPase component

Query= uniprot:Q31RN8
         (261 letters)



>FitnessBrowser__Cola:Echvi_3653
          Length = 290

 Score =  136 bits (343), Expect = 4e-37
 Identities = 74/224 (33%), Positives = 135/224 (60%), Gaps = 9/224 (4%)

Query: 41  VSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL--SHDRRDIATIRQ 98
           + LT+ +GE + + GPSGSGK++ LR ++ L +  +G + + G +   +   ++++  R+
Sbjct: 21  IKLTISQGEFITLFGPSGSGKTSTLRMISGLLTPDKGHLSVNGEQWFDASFGKNVSPGRR 80

Query: 99  EVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQL 158
           ++G +FQ ++LFP++TV +N+  A         A+ +A   +LLE + +    D  P  L
Sbjct: 81  KLGYLFQDYSLFPNMTVKENIAFALKN------AKDKAYLMELLESMGLLHLQDTLPKHL 134

Query: 159 SGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLASE-GMTMLVATHEV 217
           SGGQQQRVA+ARALA++P ILL DEP SALDP M  ++ + +  +  +  +T ++ +H+ 
Sbjct: 135 SGGQQQRVALARALALKPDILLLDEPLSALDPSMREKLQEYILAIHRKYALTTILVSHDA 194

Query: 218 GFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQIL 261
           G   +++DR++ +  G+++ +  P  FF    +    QF  +I+
Sbjct: 195 GEIIKLSDRIIELDHGKVLRQCTPKEFFGTGLTSAKFQFQGEIM 238


Lambda     K      H
   0.321    0.134    0.387 

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: 158
Number of extensions: 7
Number of successful extensions: 4
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: 261
Length of database: 290
Length adjustment: 25
Effective length of query: 236
Effective length of database: 265
Effective search space:    62540
Effective search space used:    62540
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 (21.9 bits)
S2: 47 (22.7 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