GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Skermanella stibiiresistens SB22

Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate WP_051511604.1 N825_RS05915 amino acid ABC transporter ATP-binding protein

Query= TCDB::Q88NY5
         (256 letters)



>NCBI__GCF_000576635.1:WP_051511604.1
          Length = 252

 Score =  216 bits (551), Expect = 3e-61
 Identities = 120/244 (49%), Positives = 158/244 (64%), Gaps = 7/244 (2%)

Query: 13  MISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 72
           ++S++ V+K +GD +VL     +V+ GEV+ + G SGSGKST ++C+N LE  Q+G I V
Sbjct: 14  IVSLRGVHKSFGDVEVLRGLDLDVRMGEVIALLGRSGSGKSTALRCINGLEKIQRGTITV 73

Query: 73  DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSEAEATKKGLAL 132
            G  +A    +L  LR  VG+VFQ + LFPHLT+ +N+TI+ + V G     A+      
Sbjct: 74  CGHEVARMGRDLRPLRKDVGIVFQSYNLFPHLTVEQNVTISPKLVKGVDAKTASLLAADT 133

Query: 133 LDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVSEVLDVMV 192
           L RVGL      +P QLSGGQQQRVAIARALAM+P VMLFDE TSALDPE+  EVL  M 
Sbjct: 134 LARVGLLDKRDAYPEQLSGGQQQRVAIARALAMEPKVMLFDEVTSALDPELTGEVLRAME 193

Query: 193 QLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQSARDQRTQHLLSK 252
           +LA++GMTM+ VTHE+ FARKVA+RV+FM +G I E        G  S  D      L +
Sbjct: 194 RLARDGMTMIVVTHEVAFARKVADRVVFMYRGQIRET-------GPASLLDTPQTDELKQ 246

Query: 253 ILQH 256
            L+H
Sbjct: 247 FLEH 250


Lambda     K      H
   0.319    0.134    0.383 

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: 182
Number of extensions: 6
Number of successful extensions: 1
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: 256
Length of database: 252
Length adjustment: 24
Effective length of query: 232
Effective length of database: 228
Effective search space:    52896
Effective search space used:    52896
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: 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