GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Acidovorax sp. GW101-3H11

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Ac3H11_3327 Glutamine transport ATP-binding protein GlnQ (TC 3.A.1.3.2)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3435
         (254 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3327
          Length = 249

 Score =  216 bits (550), Expect = 4e-61
 Identities = 115/239 (48%), Positives = 156/239 (65%), Gaps = 11/239 (4%)

Query: 11  KRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILLNNEELKLV 70
           K +G+H+VLK VS     G+V  IIG+SGSGKST LR IN LE   +G I +  E +   
Sbjct: 17  KSFGAHQVLKDVSTTFNTGEVTVIIGASGSGKSTLLRAINRLEPHDSGTITIGGEPV--- 73

Query: 71  ANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMSKTEAREKA 130
                     D   LQ+ RS + MVFQ FNL+ HM+ ++N+  AP  +    +T+A  +A
Sbjct: 74  --------GDDQHLLQKQRSEVGMVFQQFNLFGHMSVLDNVTLAPRRIRHTPRTQANAQA 125

Query: 131 EHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDPELVGDVLK 190
              L +VG+      YP  +SGG+QQRVAIARALAM+P+VMLFDEPTSALDPE+V +VL 
Sbjct: 126 LALLTRVGMQDHAHKYPWQLSGGQQQRVAIARALAMQPKVMLFDEPTSALDPEMVQEVLD 185

Query: 191 VMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQSERLQQFL 249
           VM+ LA+ G TM+VVTHEMGFAREVS++++F  +G +     P E   NP ++R++ F+
Sbjct: 186 VMRELARGGMTMIVVTHEMGFAREVSDRVMFFDQGRIAHDAPPAEFFNNPANDRIRAFI 244


Lambda     K      H
   0.317    0.131    0.366 

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: 188
Number of extensions: 7
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: 254
Length of database: 249
Length adjustment: 24
Effective length of query: 230
Effective length of database: 225
Effective search space:    51750
Effective search space used:    51750
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 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