GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Desulfovibrio vulgaris Hildenborough

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate 206179 DVU0753 amino acid ABC transporter, ATP-binding protein

Query= SwissProt::P54537
         (240 letters)



>MicrobesOnline__882:206179
          Length = 243

 Score =  260 bits (664), Expect = 2e-74
 Identities = 135/242 (55%), Positives = 171/242 (70%), Gaps = 3/242 (1%)

Query: 1   MIKVEKLSKSF--GKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTI 58
           MI  E + K +  G H VL +I+  IA+GEVV + GPSGSGKST +RC+N LE    G I
Sbjct: 1   MIHFEHVHKWYPSGLH-VLNDINLDIAQGEVVVICGPSGSGKSTLIRCINRLEAIQKGNI 59

Query: 59  TIKDTEITKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNVKKESKQAAQEKAE 118
            +   +I  P+TN   +R  +G VFQ F+L+PH TVLENI  AP  V+   +  A+  A 
Sbjct: 60  VVDGIDINAPRTNLTLLRAEVGFVFQQFNLYPHMTVLENITLAPTLVRNIPRAEAERTAM 119

Query: 119 DLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQV 178
           +LL KV + +K   YP +LSGGQ+QRVAIAR LAM P IMLFDEPTSALDPEM+ EVL V
Sbjct: 120 ELLEKVNIPDKAGAYPGQLSGGQQQRVAIARGLAMKPRIMLFDEPTSALDPEMINEVLDV 179

Query: 179 MKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFLEK 238
           M++L   GMTMV VTHEMGFA+EVADRV+FMDQG++VE   P  FF +P+ +R+++FL K
Sbjct: 180 MRQLAREGMTMVCVTHEMGFAREVADRVIFMDQGILVEQNTPDAFFNNPQHERSREFLSK 239

Query: 239 IL 240
           IL
Sbjct: 240 IL 241


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: 176
Number of extensions: 2
Number of successful extensions: 1
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: 243
Length adjustment: 23
Effective length of query: 217
Effective length of database: 220
Effective search space:    47740
Effective search space used:    47740
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 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