GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruA in Pseudomonas fluorescens GW456-L13

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate PfGW456L13_5073 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__pseudo13_GW456_L13:PfGW456L13_5073 PTS system,
           fructose-specific IIB component (EC 2.7.1.69) / PTS
           system, fructose-specific IIC component (EC 2.7.1.69)
          Length = 579

 Score =  809 bits (2090), Expect = 0.0
 Identities = 423/566 (74%), Positives = 475/566 (83%), Gaps = 1/566 (0%)

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

Query: 61  LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAGAAP 120
           LV   P+  +RFVGK V+++ PA+AL D  A L+R A  A V  A + A         AP
Sbjct: 61  LVTSAPVEMSRFVGKRVFQSTPAQALQDVEAVLRRGAQDAQVYAAEEAAVEPVAVVQNAP 120

Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180
           R+VAVTACPTGVAHTFMAAEALQ AA +LG+ LQVETQGSVGARNPL    IA ADVVLL
Sbjct: 121 RLVAVTACPTGVAHTFMAAEALQQAAKRLGYELQVETQGSVGARNPLSAQAIAEADVVLL 180

Query: 181 AADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKRGVY 240
           AADI+V T RFAGKKIYRCGTG+ALKQA ATL++ALAEGQ ESA +A+   A+ EK GVY
Sbjct: 181 AADIEVATERFAGKKIYRCGTGIALKQAEATLKKALAEGQQESASSAAKTTAKQEKTGVY 240

Query: 241 KHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPMLAG 299
           KHLLTGVSFMLPMVVAGGL+IALS  FGI A+K+ G+LAA L  +G D+AF LMVP+LAG
Sbjct: 241 KHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEEGTLAAALMQIGGDSAFKLMVPLLAG 300

Query: 300 YIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEALK 359
           YIAYSIADRPGLAPGM+GGLLA TLGAGFIGGI+AGF+AGYAARAI+   RLP SLEALK
Sbjct: 301 YIAYSIADRPGLAPGMIGGLLASTLGAGFIGGIIAGFLAGYAARAINRYARLPQSLEALK 360

Query: 360 PILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVDLG 419
           PIL+IPLLASL TGL+M+YVVGKPVAGMLA LT FLD MGT+NAILLG+LLGGMMCVDLG
Sbjct: 361 PILIIPLLASLFTGLVMIYVVGKPVAGMLAGLTNFLDSMGTTNAILLGVLLGGMMCVDLG 420

Query: 420 GPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKAAS 479
           GP+NKAAYAFSVGLL+S SYAPMAA MAAGMVPPIG+G+AT +ARRKFA++ER+AGKAA 
Sbjct: 421 GPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKFAQTEREAGKAAL 480

Query: 480 VLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVPNAI 539
           VLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKL APHGGLFV+ +PNAI
Sbjct: 481 VLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVLAIPNAI 540

Query: 540 NHALAYLLAIVAGSLLTGLLYAVLKR 565
           NHAL YLLAIVAGSLLT + YA++KR
Sbjct: 541 NHALLYLLAIVAGSLLTAVAYALVKR 566


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: 944
Number of extensions: 40
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: 579
Length adjustment: 36
Effective length of query: 549
Effective length of database: 543
Effective search space:   298107
Effective search space used:   298107
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