GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Pseudomonas fluorescens FW300-N2E3

Align PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized)
to candidate AO353_25595 AO353_25595 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= TCDB::Q88NY5
         (256 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25595
          Length = 254

 Score =  232 bits (591), Expect = 6e-66
 Identities = 125/251 (49%), Positives = 168/251 (66%), Gaps = 12/251 (4%)

Query: 13  MISIKNVNKWYGDFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 72
           ++   ++NK+Y  +  L D + EV++GEV+ + GPSGSGKSTL++CVN LE   KG + V
Sbjct: 4   IVKAVSLNKYYDQYHALKDINIEVEQGEVLCIIGPSGSGKSTLLRCVNQLEKIDKGGLWV 63

Query: 73  DGTSIADP----------KTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQRKVLGRSE 122
           DG  +             ++ + + R   GMVFQ F LFPH+T+ +N+     +VL RS 
Sbjct: 64  DGELVGYRVVGNKLHELNESQIARQRLATGMVFQRFNLFPHMTVLQNIVEGPCQVLKRSP 123

Query: 123 AEATKKGLALLDRVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPE 182
            EA ++ L LL RVGL+     +P +LSGGQQQRVAIARALAM P +MLFDEPTSALDPE
Sbjct: 124 KEAHEEALELLARVGLADKRNSYPIELSGGQQQRVAIARALAMRPKLMLFDEPTSALDPE 183

Query: 183 MVSEVLDVMVQLAQEGMTMMCVTHEMGFARKVANRVIFMDKGSIIEDCTKEEFFGDQSAR 242
           +V EVL VM  LAQ GMTM+ VTHE+GFAR+V+NR++FMD G I+E  + EE     S +
Sbjct: 184 LVGEVLSVMRDLAQTGMTMIVVTHELGFAREVSNRMVFMDGGQIVEAGSPEEIL--ISPQ 241

Query: 243 DQRTQHLLSKI 253
           + RTQ  +S +
Sbjct: 242 NPRTQSFISAV 252


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: 165
Number of extensions: 8
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: 256
Length of database: 254
Length adjustment: 24
Effective length of query: 232
Effective length of database: 230
Effective search space:    53360
Effective search space used:    53360
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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