Alignments for a candidate for fruII-C in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruII-C in Pseudomonas fluorescens FW300-N2E3

Align Sugar phosphotransferase system IIC component, component of Fructose-specific Enzyme I-HPr-Enzyme IIABC complex, all encoded within a single operon with genes in the order: ptsC (IIC), ptsA (IIA), ptsH (HPr), ptsI (Enzyme I) and ptsB (IIB) (characterized)
to candidate AO353_05475 AO353_05475 PTS fructose transporter subunit IIBC

Query= TCDB::Q5V5X5
         (383 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05475
          Length = 579

 Score =  297 bits (761), Expect = 4e-85
 Identities = 162/362 (44%), Positives = 225/362 (62%), Gaps = 24/362 (6%)

Query: 6   TDQNRAESALRAHVTSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGW 65
           T  +  +   +   T V + L+TGVSFM+P V  GG+ +A+++  G T   F+  G+   
Sbjct: 223 TASSGVQGPAKKEKTGVYKHLLTGVSFMLPMVVAGGLMIALSFVFGIT--AFKEPGTLAA 280

Query: 66  FLAQIGV-AGLTIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGG 124
            L QIG      +MVP+L GYIAY+IADRPGLAPG                  + G+   
Sbjct: 281 ALMQIGGDTAFKLMVPLLAGYIAYSIADRPGLAPGM-----------------IGGLLAS 323

Query: 125 EAGAGYLGAIVAGLLAGYVARFFKNLD-VPEFIQPMMPVLLIPVATMAVLTPIMLFVLGV 183
             GAG++G I+AG +AGY A+       +P+ ++ + P+L+IP+        +M++V+G 
Sbjct: 324 TLGAGFIGGIIAGFIAGYAAQAINRYARLPQSLEALKPILIIPLLASLFTGLVMIYVVGK 383

Query: 184 PVALANEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPM 243
           PVA   E LT FL SM    AI++G++LGGMM  D+GGP+NK AY F+ GL+  + YAPM
Sbjct: 384 PVAGLLESLTHFLDSMGTTNAILLGVLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAPM 443

Query: 244 AAVMIGGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVI 303
           AA M  GM+PPIGL ++ FIA  K+A    E GK+ +VLGL FI+EGAIP+AA DPLRVI
Sbjct: 444 AATMAAGMVPPIGLGIATFIARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVI 503

Query: 304 PAIVAGSAVGGATSMALGVTMPAPHGGIFVVLLS---NQPLAFLGSILLGSLVTAVVATV 360
           PA +AG A+ GA SM  G  + APHGG+FV+L+    N  L +L +I+ GSL+TAVV   
Sbjct: 504 PASIAGGALAGALSMYFGCKLMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTAVVYAA 563

Query: 361 IK 362
           +K
Sbjct: 564 VK 565


Lambda     K      H
   0.322    0.139    0.399 

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: 776
Number of extensions: 51
Number of successful extensions: 5
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: 383
Length of database: 579
Length adjustment: 33
Effective length of query: 350
Effective length of database: 546
Effective search space:   191100
Effective search space used:   191100
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: 51 (24.3 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources