GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruA in Pseudomonas putida KT2440

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate PP_0795 PP_0795 fructose PTS permease - IIBC component

Query= TCDB::Q9HY57
         (585 letters)



>lcl|FitnessBrowser__Putida:PP_0795 PP_0795 fructose PTS permease -
           IIBC component
          Length = 580

 Score =  809 bits (2089), Expect = 0.0
 Identities = 427/581 (73%), Positives = 483/581 (83%), Gaps = 5/581 (0%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60
           M +AIVTACP GQV+SVL+ARLL  AA+R GW T VE      PE +LSA QIAEADWVL
Sbjct: 1   MNIAIVTACPNGQVSSVLSARLLSAAAQRRGWSTSVEVQNTEHPERQLSAAQIAEADWVL 60

Query: 61  LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAGAAP 120
           +V   P+  ARFVGK +Y++ P++ALAD   FL  AAA A +  A   A   A  AGA  
Sbjct: 61  VVSTGPVDLARFVGKRLYQSTPSQALADREGFLDEAAANAELLAAVTGAPAAASSAGA-- 118

Query: 121 RIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVVLL 180
           RIVAVTACPTGVAHTFMAAEALQ AA QLG+ L VETQGSVGARNPL    IAAADVVLL
Sbjct: 119 RIVAVTACPTGVAHTFMAAEALQQAAQQLGYQLTVETQGSVGARNPLSAEAIAAADVVLL 178

Query: 181 AADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVA--RDEKRG 238
           AADI+V TARFAGK+IYRCGTG+ALKQARATL++ALA+  VE+   A+A     + EK G
Sbjct: 179 AADIEVPTARFAGKRIYRCGTGIALKQARATLDKALAQATVENGADAAAATTPTKSEKTG 238

Query: 239 VYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVG-DTAFVLMVPML 297
           VYKHLLTGVSFMLPMVVAGGLLIALS  FGI+AYK+ G+L A L  +G + AF LMVP+L
Sbjct: 239 VYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAYKEAGTLPAALMQIGGEAAFKLMVPLL 298

Query: 298 AGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEA 357
           AGYIA+SIADRPGLAPGM+GGLLA TLGAGFIGGIVAGF+AGY+A+AI+   RLP+SLEA
Sbjct: 299 AGYIAWSIADRPGLAPGMIGGLLASTLGAGFIGGIVAGFLAGYSAKAIARWARLPSSLEA 358

Query: 358 LKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVD 417
           LKPIL+IPLLASL TGL+M+YVVG+PVA ML  LT FLD MGT+NAILLGLLLGGMMCVD
Sbjct: 359 LKPILIIPLLASLFTGLVMIYVVGQPVAAMLEGLTHFLDSMGTTNAILLGLLLGGMMCVD 418

Query: 418 LGGPVNKAAYAFSVGLLSSHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAGKA 477
           LGGP+NKAAYAFSVGLL+S SYAPMAA MAAGMVPPIG+G+AT LARRKFA+SER+AGKA
Sbjct: 419 LGGPINKAAYAFSVGLLASSSYAPMAATMAAGMVPPIGLGIATFLARRKFAQSEREAGKA 478

Query: 478 ASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLVPN 537
           A  LGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKL APHGGLFV+L+PN
Sbjct: 479 ALALGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGLFVLLIPN 538

Query: 538 AINHALAYLLAIVAGSLLTGLLYAVLKRGAEPGLALGTSSS 578
           AINHAL YLLAIVAGSL+T ++YAV+K+     LA+  + S
Sbjct: 539 AINHALLYLLAIVAGSLVTAVVYAVIKKSERVELAVAPAKS 579


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: 926
Number of extensions: 39
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: 580
Length adjustment: 36
Effective length of query: 549
Effective length of database: 544
Effective search space:   298656
Effective search space used:   298656
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 preprint 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