GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Sulfurimonas denitrificans DSM 1251

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_011373501.1 SUDEN_RS09795 phosphate ABC transporter ATP-binding protein PstB

Query= SwissProt::P54537
         (240 letters)



>NCBI__GCF_000012965.1:WP_011373501.1
          Length = 261

 Score =  142 bits (357), Expect = 8e-39
 Identities = 87/246 (35%), Positives = 142/246 (57%), Gaps = 13/246 (5%)

Query: 2   IKVEKLSKSFGKHEV--LKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEK--PNG-- 55
           ++V+    ++ K +V  +K +S  +A+  + A+IGPSG GK+T LR  N +    PN   
Sbjct: 13  LEVKNFEFTYAKADVPSVKKLSMPVAKHNITALIGPSGCGKTTLLRSFNRMHDLYPNNKY 72

Query: 56  -GTITIKDTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQ 114
            G IT KD  I   K + +K+R  IGM+FQ    FP  ++ +N+ Y       +++    
Sbjct: 73  SGEITFKDRNILTSKEDLIKLRIQIGMIFQKPTAFP-MSIFDNVAYGLKLQGIKNRTELS 131

Query: 115 EKAEDLLRKVGLFEKRNDY----PNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPE 170
            + E  L+   ++ +  D      N LSGGQ+QR+ IARA+A+ P+++LFDEPTSALDP 
Sbjct: 132 GRVEKALKDAAIWNEVKDRLKHDANGLSGGQQQRLCIARAVAVEPEVLLFDEPTSALDPI 191

Query: 171 MVKEVLQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSK 230
               + +++ EL E  ++++IVTH M  A  V+D   FM  G ++E G  +E F++PK K
Sbjct: 192 STGGIEELIVELRER-VSIIIVTHNMQQAARVSDYTGFMYLGELIELGKTEEIFVTPKEK 250

Query: 231 RAQDFL 236
             ++++
Sbjct: 251 LTEEYI 256


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: 163
Number of extensions: 9
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: 240
Length of database: 261
Length adjustment: 24
Effective length of query: 216
Effective length of database: 237
Effective search space:    51192
Effective search space used:    51192
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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