GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Magnetospirillum magneticum AMB-1

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_083763604.1 AMB_RS09125 ABC transporter ATP-binding protein

Query= uniprot:Q1MCU2
         (292 letters)



>NCBI__GCF_000009985.1:WP_083763604.1
          Length = 257

 Score =  334 bits (856), Expect = 1e-96
 Identities = 169/255 (66%), Positives = 199/255 (78%), Gaps = 1/255 (0%)

Query: 22  MKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITFNQKSGKQY 81
           M+FGGL A+ND SF A   +ITA+IGPNGAGKTT+FNCITGFYKP +G +T +  SG   
Sbjct: 1   MRFGGLFAVNDLSFSAAPKEITAVIGPNGAGKTTLFNCITGFYKPQVGRMTLDHPSGPM- 59

Query: 82  LLERLPDFRITKEARVARTFQNIRLFSGLTVLENLLVAQHNKLMKASGYTILGLIGVGPY 141
           LLERL DF I+ +A VARTFQNIRLF+ ++VLENL+VAQH  LM+AS +++ GL+G+  Y
Sbjct: 60  LLERLDDFAISAKAGVARTFQNIRLFARMSVLENLIVAQHTTLMRASAFSLAGLLGLSRY 119

Query: 142 KREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPELLCLDEPAAG 201
            R  A A+E AR WL+K  L   AD+ AG LPYG QRRLEIARAMCTGP LLCLDEPAAG
Sbjct: 120 ARAEARAVERARHWLDKVGLTSLADEEAGSLPYGHQRRLEIARAMCTGPLLLCLDEPAAG 179

Query: 202 LNPRESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQKISDGTPDHVKN 261
           LNPRESA LN LL  IR E G  +LLIEHDMSVVMEISDH+VVL+YG+KI++G P  +K 
Sbjct: 180 LNPRESAELNRLLLDIRDENGIGLLLIEHDMSVVMEISDHIVVLDYGKKIAEGAPAAIKA 239

Query: 262 DPRVIAAYLGVEDEE 276
           DP VI AYLG  DEE
Sbjct: 240 DPAVIRAYLGEPDEE 254


Lambda     K      H
   0.318    0.136    0.386 

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: 265
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: 292
Length of database: 257
Length adjustment: 25
Effective length of query: 267
Effective length of database: 232
Effective search space:    61944
Effective search space used:    61944
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: 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