Alignments for a candidate for fruA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruA in Pseudomonas stutzeri RCH2

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component

Query= TCDB::Q9HY57
         (585 letters)



>FitnessBrowser__psRCH2:GFF3289
          Length = 579

 Score =  771 bits (1992), Expect = 0.0
 Identities = 410/575 (71%), Positives = 471/575 (81%), Gaps = 6/575 (1%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60
           M L IVTACP G VTSVL +RLL  AA RLGW T VE +        L+  QIA AD V+
Sbjct: 1   MNLLIVTACPNGMVTSVLTSRLLEAAAHRLGWSTAVEVHDPKAIGSPLTPAQIANADLVV 60

Query: 61  LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAGAAP 120
           +V   PL+  RFVGK V ++ P+EAL DP AFL+ AA  AS     DEA   A      P
Sbjct: 61  VVKTGPLSLQRFVGKRVAQSTPSEALLDPEAFLRSAADTASELQQADEAE--AAHTSGKP 118

Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180
           ++VAVTACPTGVAHTFMAAEALQ AA + G+ LQVET+GSVGARN L+   IAAADVVLL
Sbjct: 119 KLVAVTACPTGVAHTFMAAEALQQAAIRKGYDLQVETRGSVGARNVLEADVIAAADVVLL 178

Query: 181 AADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVA---RDEKR 237
           AADI+VD ARFAGK+++RCGTGVALKQ  ATL+RAL EG V S  A +   +   + EK 
Sbjct: 179 AADIEVDVARFAGKRVFRCGTGVALKQPEATLDRALEEGAVLSGNAVATSASGEKKGEKT 238

Query: 238 GVYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPM 296
           GVYKH+LTGVS+MLPMVVAGGLLIALS  FGI+A+K+ G+LAA L  +G +TAF LMVP+
Sbjct: 239 GVYKHMLTGVSYMLPMVVAGGLLIALSFVFGIEAFKEEGTLAAALMKIGGETAFQLMVPL 298

Query: 297 LAGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLE 356
           LAGYIAYSIADRPGLAPGM+GGLLAGTLGAGFIGGI+AGF+AGYAA+A+S  + LPAS+E
Sbjct: 299 LAGYIAYSIADRPGLAPGMIGGLLAGTLGAGFIGGIIAGFVAGYAAKAVSRWIPLPASIE 358

Query: 357 ALKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCV 416
           +LKPIL+IPLLASLVTGL+M+Y+VG PVA +LA LT FLD MGTSNAILLGLLLG MMCV
Sbjct: 359 SLKPILIIPLLASLVTGLVMIYIVGTPVAKLLAGLTEFLDTMGTSNAILLGLLLGTMMCV 418

Query: 417 DLGGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGK 476
           DLGGPVNKAAYAFSVGLL+S SYAPMAA MAAGMVPPIGMG+ATL+ARRKFA++ER+AGK
Sbjct: 419 DLGGPVNKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGMGIATLIARRKFAQTEREAGK 478

Query: 477 AASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVP 536
           AA VLG CFISEGAIPFAAKDPLRVIPASIAGGALTGALSM FG KL APHGGLFV+L+P
Sbjct: 479 AALVLGCCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMAFGAKLLAPHGGLFVLLIP 538

Query: 537 NAINHALAYLLAIVAGSLLTGLLYAVLKRGAEPGL 571
           NAINHAL YL+AI+AGSL+TG++YAV+K+    GL
Sbjct: 539 NAINHALLYLVAILAGSLVTGVIYAVIKQSEPQGL 573


Lambda     K      H
   0.321    0.137    0.392 

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: 940
Number of extensions: 44
Number of successful extensions: 9
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: 585
Length of database: 579
Length adjustment: 36
Effective length of query: 549
Effective length of database: 543
Effective search space:   298107
Effective search space used:   298107
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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
the source code
instructions for running GapMind on your computer

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