GapMind for catabolism of small carbon sources

 

Alignments 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.

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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:

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