GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruII-C in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_1144 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)

Query= TCDB::Q5V5X5
         (383 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1144 PTS system,
           fructose-specific IIB component (EC 2.7.1.69) / PTS
           system, fructose-specific IIC component (EC 2.7.1.69)
          Length = 579

 Score =  295 bits (755), Expect = 2e-84
 Identities = 160/357 (44%), Positives = 224/357 (62%), Gaps = 24/357 (6%)

Query: 11  AESALRAHVTSVKEDLMTGVSFMIPFVTIGGIFLAVAYAIGDTQAVFENTGSAGWFLAQI 70
           A+   +   T + + L+TGVSFM+P V  GG+ +A+++  G T   F+  G+    L QI
Sbjct: 228 AKGPAKQEKTGIYKHLLTGVSFMLPMVVAGGLMIALSFVFGIT--AFKEEGTLAAALMQI 285

Query: 71  GV-AGLTIMVPILGGYIAYAIADRPGLAPGFLLAYILQQGNVVAEAATVIGISGGEAGAG 129
           G      +MVP+L GYIAY+IADRPGLAPG                  + G+     GAG
Sbjct: 286 GGDTAFKLMVPLLAGYIAYSIADRPGLAPGM-----------------IGGLLASTLGAG 328

Query: 130 YLGAIVAGLLAGYVARFFKNLD-VPEFIQPMMPVLLIPVATMAVLTPIMLFVLGVPVALA 188
           ++G I+AG +AGY A+       +P+ ++ + P+L+IP+        +M++V+G PVA  
Sbjct: 329 FIGGIIAGFIAGYAAQAINRYARLPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAGM 388

Query: 189 NEGLTSFLQSMQGGQAIVVGLILGGMMAFDMGGPVNKVAYVFATGLITEEIYAPMAAVMI 248
             GLT FL SM    AI++G++LGGMM  D+GGP+NK AY F+ GL+  + YAPMAA M 
Sbjct: 389 LAGLTHFLDSMGTTNAILLGVLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMA 448

Query: 249 GGMIPPIGLALSNFIAPHKYAAEMYENGKSGVVLGLSFITEGAIPYAAADPLRVIPAIVA 308
            GM+PPIGL ++ FIA  K+A    E GK+ +VLGL FI+EGAIP+AA DPLRVIPA +A
Sbjct: 449 AGMVPPIGLGIATFIARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIA 508

Query: 309 GSAVGGATSMALGVTMPAPHGGIFVVLLS---NQPLAFLGSILLGSLVTAVVATVIK 362
           G A+ GA SM  G  + APHGG+FV+L+    N  L +L +I+ GSL+TAV   ++K
Sbjct: 509 GGALTGALSMYFGCKLMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTAVTYALLK 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: 771
Number of extensions: 46
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:

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 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