GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Acidovorax sp. GW101-3H11

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein

Query= SwissProt::P54537
         (240 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3200
          Length = 604

 Score =  251 bits (642), Expect = 2e-71
 Identities = 131/249 (52%), Positives = 174/249 (69%), Gaps = 10/249 (4%)

Query: 2   IKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITIK 61
           + +  +SK +G  EVLK+++ T+  G V  ++GPSGSGKST LR +N LE+ +GG I I 
Sbjct: 356 VTIHGVSKRYGALEVLKDVTLTVLPGSVTVILGPSGSGKSTLLRSINHLERVDGGFIAID 415

Query: 62  ----------DTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQ 111
                     D      + + LK R ++GMVFQ+F+LFPH TVLENI+ APV V+K ++ 
Sbjct: 416 GELIGYRQDADALYELGENDILKRRVDVGMVFQNFNLFPHLTVLENIVEAPVTVRKLARA 475

Query: 112 AAQEKAEDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEM 171
            A+  A +LL +VGL +K + YP +LSGGQ+QRVAIARALA+ P ++LFDEPTSALDPE+
Sbjct: 476 EAEALALELLARVGLSDKAHSYPRQLSGGQQQRVAIARALALKPKVLLFDEPTSALDPEL 535

Query: 172 VKEVLQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKR 231
           V EVL V+KEL  TG T+VIVTHE+GFA+EVAD V+FM+QG +VE G P + F  P   R
Sbjct: 536 VGEVLDVIKELARTGTTLVIVTHEIGFAREVADTVVFMEQGRVVETGTPAKVFSQPDHPR 595

Query: 232 AQDFLEKIL 240
              FL K+L
Sbjct: 596 TAAFLAKVL 604


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: 306
Number of extensions: 8
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: 604
Length adjustment: 30
Effective length of query: 210
Effective length of database: 574
Effective search space:   120540
Effective search space used:   120540
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: 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