Aligments for a candidate for fruA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruA in Pseudomonas simiae WCS417

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate GFF782 PS417_03975 FruA

Query= TCDB::Q9HY57
         (585 letters)



>FitnessBrowser__WCS417:GFF782
          Length = 569

 Score =  781 bits (2017), Expect = 0.0
 Identities = 411/565 (72%), Positives = 469/565 (83%), Gaps = 8/565 (1%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60
           MKLAIVTACP G VTSVL ARLL  AA+R GW T VE     RPE +LS   I +A+WVL
Sbjct: 1   MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDVQRPERQLSQATIDDAEWVL 60

Query: 61  LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAGAAP 120
           LV   P+   RFVGK V+++ PA+ALAD  A L+R A  A V VA  +A      A  AP
Sbjct: 61  LVSSTPVDMQRFVGKRVFQSTPAQALADVDAVLRRGAEEAQVYVATQQA------AENAP 114

Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180
           RIVA+TACPTGVAHTFMAAEALQ  A +LG+ LQVETQGSVGAR PL P  IA ADVVLL
Sbjct: 115 RIVAITACPTGVAHTFMAAEALQQTAKRLGYDLQVETQGSVGARTPLSPQAIAEADVVLL 174

Query: 181 AADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKRGVY 240
           AADI+V T RFAGKKIYRCGTG+ALKQ+ ATL +ALAEG VESA  AS  VA+ EK GVY
Sbjct: 175 AADIEVATERFAGKKIYRCGTGIALKQSEATLNKALAEGAVESA--ASGAVAKKEKTGVY 232

Query: 241 KHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVGDTAFVLMVPMLAGY 300
           KHLLTGVSFMLPMVVAGGLLIALS  FGI A+++ G+LAA L+TVGD AF+LMVP+LAGY
Sbjct: 233 KHLLTGVSFMLPMVVAGGLLIALSFMFGITAFEEKGTLAAALKTVGDQAFMLMVPLLAGY 292

Query: 301 IAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEALKP 360
           IAYSIADRP LAPGM+GGLLA TLGAGFIGGI AGF+AGY  + I+  ++LP SL+ALKP
Sbjct: 293 IAYSIADRPALAPGMIGGLLATTLGAGFIGGIFAGFLAGYCVKLITRAVQLPQSLDALKP 352

Query: 361 ILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVDLGG 420
           IL+IPLLASL TGL M+Y+VG PVA ML  LT FL+ MGT+NA+LLG+LLGGMMCVDLGG
Sbjct: 353 ILIIPLLASLFTGLAMIYLVGPPVARMLVGLTEFLNTMGTTNAVLLGILLGGMMCVDLGG 412

Query: 421 PVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKAASV 480
           P+NKAAYAFSVG+L++HS AP+AA MAAGMVPPIGMG+AT LARRKFA++ER+AGKAA +
Sbjct: 413 PINKAAYAFSVGMLAAHSGAPIAATMAAGMVPPIGMGIATFLARRKFAQTEREAGKAAII 472

Query: 481 LGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVPNAIN 540
           LG+ FISEGAIPFAAKDPLRVIPASIAGGAL GALSMYFGCKL APHGGL V+++PNA+N
Sbjct: 473 LGMVFISEGAIPFAAKDPLRVIPASIAGGALAGALSMYFGCKLAAPHGGLAVLVIPNAMN 532

Query: 541 HALAYLLAIVAGSLLTGLLYAVLKR 565
           HAL YLLAIVAGSLLTGL+YA++KR
Sbjct: 533 HALLYLLAIVAGSLLTGLVYALIKR 557


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: 925
Number of extensions: 39
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: 585
Length of database: 569
Length adjustment: 36
Effective length of query: 549
Effective length of database: 533
Effective search space:   292617
Effective search space used:   292617
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.

Downloads

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

Related tools

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