GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08250 in Pantoea rwandensis LMG 26275

Align Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_084931715.1 HA51_RS02580 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ1
         (236 letters)



>NCBI__GCF_002095475.1:WP_084931715.1
          Length = 234

 Score =  145 bits (365), Expect = 9e-40
 Identities = 78/214 (36%), Positives = 130/214 (60%), Gaps = 5/214 (2%)

Query: 1   MLKVSGVHTFYGAIEALKGVDIEIGAGEIVSLIGANGAGKSTLLMTICGSPRARMGRITF 60
           ML++  + + Y  I  L   ++ +GA     ++G NG GK+TLL TI G   A  G I  
Sbjct: 1   MLEIKEMVSGYNKIPVLHLSELFVGAKSFTGVLGRNGMGKTTLLRTIMGELPAWQGSIAL 60

Query: 61  EGQDITQMPTYELVRLGIAQSPEGRRIFPRMSVLENLQMGSIT--AKPGSFANELERVLT 118
            G DIT+   ++    GI   P+GR+IFP ++V ENL+MG +   ++ G+    +E++L 
Sbjct: 61  NGIDITRYQAHQRAVAGIGFVPQGRQIFPLLTVEENLRMGCVKHFSRAGTI---IEQMLE 117

Query: 119 LFPRLKERISQRAGTMSGGEQQMLAIGRALMSQPRLLLLDEPSLGLAPLVVKQIFQAVKD 178
           +FPRLK  ++Q  G +SGGEQQ+LA+ R L  QP+L+LLDEP+ G+ P + ++I + ++ 
Sbjct: 118 IFPRLKRLLTQPGGALSGGEQQLLALARCLCGQPQLVLLDEPTEGIQPNICEEIIETLQR 177

Query: 179 INREQKMTVFMVEQNAFHALKLAHRGYVMVNGKV 212
           +  E  +++ +VEQ+      L+ R +V+  G++
Sbjct: 178 LRHEMDISIILVEQDIEFLYALSDRIHVIEKGQI 211


Lambda     K      H
   0.320    0.136    0.377 

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: 170
Number of extensions: 9
Number of successful extensions: 2
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: 236
Length of database: 234
Length adjustment: 23
Effective length of query: 213
Effective length of database: 211
Effective search space:    44943
Effective search space used:    44943
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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