GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Azospirillum brasilense Sp245

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate AZOBR_RS23525 AZOBR_RS23525 ABC transporter ATP-binding protein

Query= SwissProt::P54537
         (240 letters)



>FitnessBrowser__azobra:AZOBR_RS23525
          Length = 269

 Score =  254 bits (650), Expect = 9e-73
 Identities = 135/245 (55%), Positives = 168/245 (68%), Gaps = 5/245 (2%)

Query: 1   MIKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITI 60
           +I++  + KSFG  EVLK++S T+       VIGPSGSGKST LRC N LE  + G I I
Sbjct: 1   VIEIRNVYKSFGSTEVLKDVSLTVPPSRTTVVIGPSGSGKSTLLRCCNCLETADRGEIRI 60

Query: 61  KDTEITK-----PKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQE 115
               I       P      +R   GMVFQ F+LFPH T +EN+M APV V+  +K  A+E
Sbjct: 61  NHRTIIADGKPLPDKELNALRAETGMVFQSFNLFPHMTTVENVMRAPVVVRGMAKAEARE 120

Query: 116 KAEDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEV 175
            A +LLRKVGL +K + YP+ LSGGQKQR AIARALAM P +MLFDEPTSALDPE+V EV
Sbjct: 121 LAMELLRKVGLGDKADVYPSTLSGGQKQRAAIARALAMKPKVMLFDEPTSALDPELVGEV 180

Query: 176 LQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDF 235
           LQVMK L E GMTM++VTHEMGFA+EVAD V+ M  G IVE G+P++ F +P  +R + F
Sbjct: 181 LQVMKTLAEEGMTMMVVTHEMGFAREVADTVVVMADGRIVESGSPEQIFTNPTQERTRGF 240

Query: 236 LEKIL 240
           L  ++
Sbjct: 241 LRALV 245


Lambda     K      H
   0.317    0.134    0.368 

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: 203
Number of extensions: 6
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: 240
Length of database: 269
Length adjustment: 24
Effective length of query: 216
Effective length of database: 245
Effective search space:    52920
Effective search space used:    52920
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 (21.6 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