GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Erythrobacter gangjinensis K7-2

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate WP_047006469.1 AAW01_RS01810 phosphate ABC transporter ATP-binding protein

Query= SwissProt::P54537
         (240 letters)



>NCBI__GCF_001010925.1:WP_047006469.1
          Length = 280

 Score =  144 bits (363), Expect = 2e-39
 Identities = 90/236 (38%), Positives = 135/236 (57%), Gaps = 12/236 (5%)

Query: 11  FGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEK--PNG---GTITIKDTEI 65
           +G    + ++S  I    V A IGPSG GKSTFLR LN +    P+    G I +   +I
Sbjct: 42  YGDKRAIDDVSIDIYTEYVTAFIGPSGCGKSTFLRALNRMNDTIPSASVKGRIELDGDDI 101

Query: 66  TKPKTNTLKVRENIGMVFQHFHLFPHKTVLENIMYAP-VNVKKESKQAAQEKAEDLLRKV 124
                + +++R  +GMVFQ  + FP K++ ENI Y P ++   E++    E  E  LR+ 
Sbjct: 102 YASGMDVVQLRARVGMVFQKPNPFP-KSIYENIAYGPRIHGLAENRNDVDEIVEKSLRRA 160

Query: 125 GLFE----KRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPEMVKEVLQVMK 180
           GL+E    +  D    LSGGQ+QR+ IARA+A++P+++L DEP SALDP    ++ +++ 
Sbjct: 161 GLWEEVKDRLQDSGTALSGGQQQRLCIARAIAVDPEVILMDEPCSALDPIATAKIEELID 220

Query: 181 ELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKEFFMSPKSKRAQDFL 236
           EL      +VIVTH M  A  V+ R  F   G +VE G+  + F +P+ KR QD++
Sbjct: 221 EL-RGRYGIVIVTHSMQQAARVSQRTAFFHLGKMVEYGHTSDIFTNPREKRTQDYI 275


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: 162
Number of extensions: 11
Number of successful extensions: 5
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: 280
Length adjustment: 24
Effective length of query: 216
Effective length of database: 256
Effective search space:    55296
Effective search space used:    55296
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 24 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