GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hisP in Pseudomonas fluorescens FW300-N2E2

Align Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale)
to candidate Pf6N2E2_5567 Glutamate Aspartate transport ATP-binding protein GltL (TC 3.A.1.3.4)

Query= uniprot:Q88GX0
         (260 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5567
          Length = 244

 Score =  276 bits (706), Expect = 3e-79
 Identities = 139/242 (57%), Positives = 179/242 (73%), Gaps = 2/242 (0%)

Query: 20  LIRIEGLNKHYGAFHVLRDIDLQVREGERIVLCGPSGSGKSTLIRCINRLEVAQQGSIQV 79
           +I I+ +NK YG F VL +   +V +GE +V+CGPSGSGKSTLI+C+N LE  Q+G I V
Sbjct: 1   MISIKNINKWYGDFQVLTNCSTEVSKGEVVVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60

Query: 80  DGIDLAATTREAAQVRSDIGMVFQHFNLFPHMSVLDNCLLAPTSVRGLSRKDAEERARMY 139
           DG  +A       ++RS +GMVFQHF LFPH+++ +N  +A   V G S+++A ++    
Sbjct: 61  DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120

Query: 140 LSKVGIESQAHKYPSQLSGGQQQRVAIARALCMKPRIMLFDEPTSALDPEMVAEVLDVLV 199
           L +VG+ + AHK+P QLSGGQQQRVAIARAL M P +MLFDEPTSALDPEMV EVLDV+V
Sbjct: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPVVMLFDEPTSALDPEMVNEVLDVMV 180

Query: 200 QLAGTGMTMLCVTHEMGFARQVAERVLFLEGGQIIEDSPPQVFFN--QPRTERAKAFLAQ 257
           QLA  GMTM+CVTHEMGFAR+VA RV+F++ GQIIED   + FF     R+ERA+ FL +
Sbjct: 181 QLAHEGMTMMCVTHEMGFARKVANRVIFMDQGQIIEDCKKEEFFGDISARSERAQHFLEK 240

Query: 258 IL 259
           IL
Sbjct: 241 IL 242


Lambda     K      H
   0.322    0.137    0.395 

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: 204
Number of extensions: 5
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: 260
Length of database: 244
Length adjustment: 24
Effective length of query: 236
Effective length of database: 220
Effective search space:    51920
Effective search space used:    51920
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 (21.9 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