GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2555 in Magnetovibrio blakemorei MV-1

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate WP_139134956.1 BEN30_RS09695 transporter substrate-binding domain-containing protein

Query= reanno::acidovorax_3H11:Ac3H11_2555
         (249 letters)



>NCBI__GCF_001746755.1:WP_139134956.1
          Length = 244

 Score =  107 bits (266), Expect = 3e-28
 Identities = 72/241 (29%), Positives = 121/241 (50%), Gaps = 6/241 (2%)

Query: 7   LLLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFVE-NGKRTGFDIELVEAIAKTMGK 65
           + +A+L+  A   T A A D  LR+GT+  +PP   V+ NG+  GFD+++ +A+  +M  
Sbjct: 1   MAIATLSVIALTAT-AYAADK-LRIGTEGAYPPFNLVDSNGELQGFDVDIAKALCASMKA 58

Query: 66  QVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKAI 125
           +  +V  D+ G+IP L  ++FD  V+++ IT+ER+K VDF++ YY   L  + K      
Sbjct: 59  ECTFVKQDWDGMIPALNKRKFDAIVASMSITEERQKAVDFSERYYTNKLQFVGKKGMDVD 118

Query: 126 NKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVTGKPAA 185
              A L GK +  Q  T S  +L +          +  +  +  +  GR DA +      
Sbjct: 119 ISAAGLKGKVIGAQRATISGQWLEQNRADADIKLYDTQENAYLDLASGRLDAILADAFVN 178

Query: 186 FQYVRTRPGLRVL---DEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKKW 242
           ++++ +  G       D     +  G+A+RK   +L   +N AI  + ADGTY  I  K+
Sbjct: 179 YEWLNSDAGNAFEAKGDPVFDGDLIGIAIRKGEDDLRIKLNKAIKDIVADGTYGKINAKY 238

Query: 243 F 243
           F
Sbjct: 239 F 239


Lambda     K      H
   0.317    0.133    0.369 

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: 174
Number of extensions: 11
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: 249
Length of database: 244
Length adjustment: 24
Effective length of query: 225
Effective length of database: 220
Effective search space:    49500
Effective search space used:    49500
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 (21.7 bits)
S2: 46 (22.3 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