Alignments for a candidate for fruA in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruA in Pseudomonas benzenivorans DSM 8628

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate WP_090448051.1 BLS63_RS22565 fructose-specific PTS transporter subunit EIIC

Query= TCDB::Q9HY57
         (585 letters)



>NCBI__GCF_900100495.1:WP_090448051.1
          Length = 577

 Score =  780 bits (2014), Expect = 0.0
 Identities = 420/577 (72%), Positives = 473/577 (81%), Gaps = 8/577 (1%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60
           M L IVTACP G VTSVL +RLL  AA+RLGW T VE +        L  E IA AD VL
Sbjct: 1   MNLLIVTACPNGMVTSVLCSRLLEAAAQRLGWSTRVEVHDPRAIGSPLREEDIAAADLVL 60

Query: 61  LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAGAAP 120
           +V    L   RFVGK + ++ PAEAL DP+ FL+ AA  A V +A + A   A +    P
Sbjct: 61  VVKTGELPLQRFVGKRLLQSTPAEALVDPQQFLREAAEQAQV-LAAEPAAAAATDK---P 116

Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180
           R+VAVTACPTGVAHTFMAAEALQ AA QLG+ LQVET+GSVGARN LD A IAAAD VLL
Sbjct: 117 RLVAVTACPTGVAHTFMAAEALQQAAEQLGYDLQVETRGSVGARNLLDDAAIAAADAVLL 176

Query: 181 AADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEG-QVESAGAASAVVARDE--KR 237
           AADI+VDTARFAGKK++RCGTGVALKQ R TLERALAEG  + + G A A  A     + 
Sbjct: 177 AADIEVDTARFAGKKVFRCGTGVALKQPRQTLERALAEGVPLAATGKAEAAPASQSAGQA 236

Query: 238 GVYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPM 296
           G YKHLLTGVS+MLPMVVAGGLLIALS  FGI+A+KQ GSLAA L  +G D AF LMVP+
Sbjct: 237 GPYKHLLTGVSYMLPMVVAGGLLIALSFVFGIEAFKQEGSLAAALMQIGGDAAFKLMVPV 296

Query: 297 LAGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLE 356
           LAGYIAYSIADRPGLAPGM+GGLLA +LGAGFIGGIVAGF+AGY A+AI+  ++LPAS+E
Sbjct: 297 LAGYIAYSIADRPGLAPGMIGGLLASSLGAGFIGGIVAGFLAGYTAKAIARWVQLPASVE 356

Query: 357 ALKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCV 416
           ALKPIL+IPLLASL TGL+M+YVVG+PVAGMLA LT FLDGMG++NAILLGLLLGGMMCV
Sbjct: 357 ALKPILIIPLLASLFTGLVMIYVVGQPVAGMLAGLTAFLDGMGSTNAILLGLLLGGMMCV 416

Query: 417 DLGGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGK 476
           DLGGP+NKAAYAFSVGLL+S SYAPMAAVMAAGMVPPIGM +A++LAR KFA+SER+AGK
Sbjct: 417 DLGGPINKAAYAFSVGLLASQSYAPMAAVMAAGMVPPIGMAIASVLARHKFAQSEREAGK 476

Query: 477 AASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVP 536
           AA VLGLCFISEGAIPFAAKDP RVIPASIAGGALTGALSMYFGCKL APHGGLFV+L+P
Sbjct: 477 AAGVLGLCFISEGAIPFAAKDPFRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVLLIP 536

Query: 537 NAINHALAYLLAIVAGSLLTGLLYAVLKRGAEPGLAL 573
           NAINHA  YLLAIVAGSLLTG+ YA++KR     LA+
Sbjct: 537 NAINHAALYLLAIVAGSLLTGVAYALIKRADAQPLAV 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: 994
Number of extensions: 50
Number of successful extensions: 7
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: 577
Length adjustment: 36
Effective length of query: 549
Effective length of database: 541
Effective search space:   297009
Effective search space used:   297009
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 Apr 09 2024. 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)
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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 2024 update 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