GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fruA in Marinobacter adhaerens HP15

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component

Query= TCDB::Q9HY57
         (585 letters)



>lcl|FitnessBrowser__Marino:GFF3783 HP15_3725 PTS system,
           fructose-specific IIBC component
          Length = 587

 Score =  634 bits (1636), Expect = 0.0
 Identities = 349/578 (60%), Positives = 420/578 (72%), Gaps = 12/578 (2%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANA-GSRPEGELSAEQIAEADWV 59
           M L IVTACP G  T  LAAR L  AA R GW    +      + + + S   I +AD V
Sbjct: 1   MNLIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLV 60

Query: 60  LLVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASV---EVAGDEAGLVAPEA 116
           +     P+    + GK + +     AL DP A L RA A A+     +A  E+   +   
Sbjct: 61  IAAVGIPVNLDVYAGKRLLQIPVTAALPDPDAILTRAQAEATPWDPAMASQESIATSTAV 120

Query: 117 G---AAPRIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIA 173
           G   A  RIVAVTACPTGVAHTFMAAEAL  AA   G  ++VETQGSVGA++PL   +IA
Sbjct: 121 GSTSAGKRIVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIA 180

Query: 174 AADVVLLAADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGA--ASAVV 231
           AADVV+LA DI+VD  RF+GK+++R  TG ALK+   T+  AL +  V +AG    S   
Sbjct: 181 AADVVILACDIEVDPGRFSGKRVWRTSTGAALKKPADTIRDALEQAVVLNAGQKKTSGAS 240

Query: 232 ARDEKRGVYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVGD-TAF 290
              EK+G YKHLLTGVSFMLPMVVAGGLLIALS  FGI+A+++ G+LAA L  +G  TAF
Sbjct: 241 GSGEKKGPYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAFQEEGTLAAALMQIGGGTAF 300

Query: 291 VLMVPMLAGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLR 350
            LM+P+LAGYIA+SIADRPGLAPGM+GG LAG LGAGF+GGIVAGF+AGY AR IS  L 
Sbjct: 301 KLMIPLLAGYIAWSIADRPGLAPGMIGGFLAGELGAGFLGGIVAGFLAGYVARFISQKLP 360

Query: 351 LPASLEALKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLL 410
           +P S+E+LKPIL+IPLLASLVTGL M+YV+G+P+A ++ ALTGFL+GMGT+NAILLG +L
Sbjct: 361 MPESIESLKPILIIPLLASLVTGLGMIYVIGEPMAAIMGALTGFLEGMGTTNAILLGGIL 420

Query: 411 GGMMCVDLGGPVNKAAYAFSVGLLS--SHSYAPMAAVMAAGMVPPIGMGLATLLARRKFA 468
           G MMC DLGGPVNKAAY F VGLLS  S   APMAA+MAAGMVP IGMG+A+ +ARRKFA
Sbjct: 421 GAMMCFDLGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMAAGMVPAIGMGVASFIARRKFA 480

Query: 469 ESERQAGKAASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHG 528
           E+ERQAG+A+ VLGLCFISEGAIPF AKDPLRVIP  + GGA+TGALSM F  KL APHG
Sbjct: 481 EAERQAGRASFVLGLCFISEGAIPFMAKDPLRVIPVCMIGGAITGALSMLFTVKLMAPHG 540

Query: 529 GLFVMLVPNAINHALAYLLAIVAGSLLTGLLYAVLKRG 566
           GLFV+ +PNA++  L YL+AI  GSL+ G  YA+LK G
Sbjct: 541 GLFVLAIPNAVSAVLPYLIAIAVGSLVIGFGYALLKTG 578


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: 923
Number of extensions: 44
Number of successful extensions: 9
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: 587
Length adjustment: 37
Effective length of query: 548
Effective length of database: 550
Effective search space:   301400
Effective search space used:   301400
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