GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artP in Pedobacter sp. GW460-11-11-14-LB5

Align Arginine transport ATP-binding protein ArtM (characterized)
to candidate CA265_RS16020 CA265_RS16020 ABC transporter ATP-binding protein

Query= SwissProt::P54537
         (240 letters)



>FitnessBrowser__Pedo557:CA265_RS16020
          Length = 250

 Score =  146 bits (369), Expect = 3e-40
 Identities = 88/228 (38%), Positives = 138/228 (60%), Gaps = 10/228 (4%)

Query: 1   MIKVEKLSKSFGKHEVLKNISTTIAEGEVVAVIGPSGSGKSTFLRCLNLLEKPNGGTITI 60
           MI+++ + KSF  ++VL+ IS    EG    +IG SGSGK+T L+C+  L +P+ G++  
Sbjct: 1   MIEIKDIYKSFSGNDVLQGISGKFEEGVTNLIIGGSGSGKTTLLKCMVGLHQPDSGSVLY 60

Query: 61  KDTEITKPKT--NTLKVRENIGMVFQHFHLFPHKTVLENIMYAPVNV-KKESKQAAQEKA 117
              + T P T    ++VR+ IGM+FQ   LF   TV ENIM+ P+N+   +S++   E+ 
Sbjct: 61  DGRDFT-PMTYEQRIEVRKEIGMLFQGSALFDSMTVEENIMF-PLNMFTDQSRKEKLERV 118

Query: 118 EDLLRKVGLFEKRNDYPNRLSGGQKQRVAIARALAMNPDIMLFDEPTSALDPE---MVKE 174
           +  L +V L  K   +P  LSGG K+RV IARA++MNP  +  DEP S LDP+   ++ E
Sbjct: 119 DFCLERVNLAGKNKLFPAELSGGMKKRVGIARAISMNPKYLFCDEPNSGLDPKTSIVIDE 178

Query: 175 VLQVMKELVETGMTMVIVTHEMGFAKEVADRVLFMDQGMIVEDGNPKE 222
           ++Q + E  +T  T ++VTH+M     + D +LF+ +G    +G+ KE
Sbjct: 179 LIQEITEEYKT--TTIVVTHDMNSVMGIGDYILFLHEGKKFWEGSNKE 224


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: 194
Number of extensions: 15
Number of successful extensions: 3
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: 250
Length adjustment: 24
Effective length of query: 216
Effective length of database: 226
Effective search space:    48816
Effective search space used:    48816
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