Alignments for a candidate for fruA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruA in Pseudomonas fluorescens FW300-N2C3

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate AO356_07325 AO356_07325 PTS fructose transporter subunit IIBC

Query= TCDB::Q9HY57
         (585 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07325
          Length = 580

 Score =  804 bits (2076), Expect = 0.0
 Identities = 422/575 (73%), Positives = 477/575 (82%), Gaps = 2/575 (0%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60
           MKLAIVTACP G VTSVL ARLL  AA+R GW T VE +  + PE +LSA  +  A+WVL
Sbjct: 1   MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVL 60

Query: 61  LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLV-APEAGAA 119
           LV   P+  +RFVGK V+R+ PA AL D  A L+R A  A V    D +  V A  A  A
Sbjct: 61  LVASGPVDLSRFVGKRVFRSTPALALQDVDAVLRRGAVEAEVLGEADASAQVPAASAERA 120

Query: 120 PRIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVL 179
           PR+VA+TACPTGVAHTFMAAEALQ AA +LG+ LQVETQGSVGARNPL    IA ADVVL
Sbjct: 121 PRLVAITACPTGVAHTFMAAEALQQAATKLGYDLQVETQGSVGARNPLSAEAIAEADVVL 180

Query: 180 LAADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKRGV 239
           LA DI+V T RFAGKKIYRCGTG+ALKQA ATL +AL E + ESA + ++  A+ EK G 
Sbjct: 181 LATDIEVATERFAGKKIYRCGTGIALKQAEATLNKALVEARQESASSGASAPAKSEKTGA 240

Query: 240 YKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPMLA 298
           YKHLLTGVSFMLPMVVAGGL+IALS  FGI+A+K+PG+LAA L  +G +TAF LMVP+LA
Sbjct: 241 YKHLLTGVSFMLPMVVAGGLMIALSFVFGIEAFKEPGTLAAALMQIGGETAFKLMVPLLA 300

Query: 299 GYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEAL 358
           GYIAYSIADRPGLAPGM+GG+LA TLGAGFIGGI+AGF+AGYAA+AIS   RLP SLEAL
Sbjct: 301 GYIAYSIADRPGLAPGMIGGMLASTLGAGFIGGIIAGFLAGYAAKAISRYARLPQSLEAL 360

Query: 359 KPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVDL 418
           KPIL+IPLLASL TGL+M+Y+VGKPVAGML ALT FLD MGT+NAILLG+LLG MMCVDL
Sbjct: 361 KPILIIPLLASLFTGLVMIYIVGKPVAGMLEALTHFLDSMGTTNAILLGVLLGAMMCVDL 420

Query: 419 GGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKAA 478
           GGP+NKAAYAFSVGLL+S SYAPMAA MAAGMVPPIG+G+AT +ARRKFA++ER+AGKAA
Sbjct: 421 GGPINKAAYAFSVGLLASQSYAPMAAAMAAGMVPPIGLGIATFIARRKFAQTEREAGKAA 480

Query: 479 SVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVPNA 538
            VLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKL APHGGLFVML+PNA
Sbjct: 481 LVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVMLIPNA 540

Query: 539 INHALAYLLAIVAGSLLTGLLYAVLKRGAEPGLAL 573
           INHAL YLLAIVAGSLLT + YA+LKR     +AL
Sbjct: 541 INHALLYLLAIVAGSLLTAVAYALLKRPEVVEMAL 575


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: 945
Number of extensions: 38
Number of successful extensions: 6
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: 580
Length adjustment: 36
Effective length of query: 549
Effective length of database: 544
Effective search space:   298656
Effective search space used:   298656
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