GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruA in Pseudomonas fluorescens FW300-N2E2

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate Pf6N2E2_3337 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)

Query= TCDB::Q9HY57
         (585 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3337 PTS system,
           fructose-specific IIB component (EC 2.7.1.69) / PTS
           system, fructose-specific IIC component (EC 2.7.1.69)
          Length = 575

 Score =  797 bits (2058), Expect = 0.0
 Identities = 417/570 (73%), Positives = 473/570 (82%), Gaps = 2/570 (0%)

Query: 6   VTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVLLVGVE 65
           VTACP G VTSVL ARLL  AA+R GW T VE +  + PE +LSA  +  A+WVLLV   
Sbjct: 1   VTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVLLVASG 60

Query: 66  PLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLV-APEAGAAPRIVA 124
           P+  +RFVGK ++R+ PA AL D  + L+R A  A V +A D      A     APR+VA
Sbjct: 61  PVDMSRFVGKRLFRSTPALALQDVDSVLRRGAEEAEVFLASDVVEQAPAVSTDRAPRLVA 120

Query: 125 VTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLLAADI 184
           +TACPTGVAHTFMAAEALQ AA +LG+ LQVETQGSVGARNPL    IA ADVVLLA DI
Sbjct: 121 ITACPTGVAHTFMAAEALQQAATKLGYDLQVETQGSVGARNPLSAEAIAEADVVLLATDI 180

Query: 185 DVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKRGVYKHLL 244
           +V T RFAGKKIYRC TG+ALKQA ATL +AL EG+ ESA + ++  A+ EK GVYKHLL
Sbjct: 181 EVATERFAGKKIYRCSTGIALKQAEATLNKALVEGRQESASSGASAPAKSEKTGVYKHLL 240

Query: 245 TGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPMLAGYIAY 303
           TGVSFMLPMVVAGGL+IALS  FGI+A+K+PG+LAA L  +G DTAF LMVP+LAGYIAY
Sbjct: 241 TGVSFMLPMVVAGGLMIALSFVFGIEAFKEPGTLAAALMQIGGDTAFKLMVPLLAGYIAY 300

Query: 304 SIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEALKPILV 363
           SIADRPGLAPGM+GG+LA TLGAGFIGGI+AGF+AGYAA+AIS   RLP SLEALKPIL+
Sbjct: 301 SIADRPGLAPGMIGGMLASTLGAGFIGGIIAGFLAGYAAKAISRYARLPQSLEALKPILI 360

Query: 364 IPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVDLGGPVN 423
           IPLLASL TGL+M+Y+VGKPVAGML ALT FLD MGT+NAILLG+LLG MMCVDLGGP+N
Sbjct: 361 IPLLASLFTGLVMIYIVGKPVAGMLEALTHFLDSMGTTNAILLGVLLGAMMCVDLGGPIN 420

Query: 424 KAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKAASVLGL 483
           KAAYAFSVGLL+S SYAPMAA MAAGMVPPIG+G+AT +ARRKFA++ER+AGKAA VLGL
Sbjct: 421 KAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKFAQTEREAGKAALVLGL 480

Query: 484 CFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVPNAINHAL 543
           CFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKL APHGGLFVML+PNAINHAL
Sbjct: 481 CFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVMLIPNAINHAL 540

Query: 544 AYLLAIVAGSLLTGLLYAVLKRGAEPGLAL 573
            YLLAIVAGSLLTG+ YA+LKR     +AL
Sbjct: 541 LYLLAIVAGSLLTGVAYALLKRPEVVEMAL 570


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: 933
Number of extensions: 40
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 585
Length of database: 575
Length adjustment: 36
Effective length of query: 549
Effective length of database: 539
Effective search space:   295911
Effective search space used:   295911
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 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