GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruA in Marinobacter algicola DG893

Align Phosphotransferase system transporter fructose-specific IIBC component, FruA, component of Fructose-specific PTS permease, FruIIBC/FruI-HPr-IIA (characterized)
to candidate WP_007154191.1 MDG893_RS12700 PTS fructose-like transporter subunit IIB

Query= TCDB::Q9HY57
         (585 letters)



>NCBI__GCF_000170835.1:WP_007154191.1
          Length = 579

 Score =  626 bits (1615), Expect = 0.0
 Identities = 340/571 (59%), Positives = 410/571 (71%), Gaps = 6/571 (1%)

Query: 1   MKLAIVTACPGGQVTSVLAARLLRGAAERLGWETCVEANAGSRPEGELSAEQIAEADWVL 60
           MKL IVTACP G  TS LAAR L  A+++ GWE   +  +  +P   L  + IA AD V+
Sbjct: 1   MKLIIVTACPQGVATSFLAARALERASQQKGWEARTDIRSPQQPLSSLPVDVIASADLVV 60

Query: 61  LVGVEPLAAARFVGKPVYRARPAEALADPRAFLQRAAALASVEVAGDEAGLVAPEAG--A 118
                P     + GK +Y+     AL D  A L +A   A       EA    P A   A
Sbjct: 61  AATGTPTDLNAYAGKRLYQIPVTAALPDAAAVLDQAEKQAEPYQL-TEASQPEPAASGNA 119

Query: 119 APRIVAVTACPTGVAHTFMAAEALQLAAGQLGFALQVETQGSVGARNPLDPADIAAADVV 178
             RIVAVTACPTGVAHTFMAAEAL  AA   G  ++VETQGSVGA++PL   +I AADVV
Sbjct: 120 GQRIVAVTACPTGVAHTFMAAEALTAAATAAGHQIRVETQGSVGAQDPLTAEEIEAADVV 179

Query: 179 LLAADIDVDTARFAGKKIYRCGTGVALKQARATLERALAEGQVESAGAASAVVARDEKRG 238
           +LA DI+VD +RFAGK+++R  TG ALK+   T++ A+    VE     +      EKRG
Sbjct: 180 ILACDIEVDPSRFAGKRLWRTSTGSALKKPGPTIDDAMTNASVEEGQKKATSGGGGEKRG 239

Query: 239 VYKHLLTGVSFMLPMVVAGGLLIALSLAFGIDAYKQPGSLAAVLRTVGD-TAFVLMVPML 297
            YKHLLTGVSFMLPMVVAGGLLIALS  FGIDA+++ G+LAA L  +G   AF LM+P+L
Sbjct: 240 PYKHLLTGVSFMLPMVVAGGLLIALSFVFGIDAFEEEGTLAAALMQIGGGAAFQLMIPLL 299

Query: 298 AGYIAYSIADRPGLAPGMLGGLLAGTLGAGFIGGIVAGFIAGYAARAISHGLRLPASLEA 357
           AGYIA+SIADRPGLAPGM+GG LA TLGAGF+GGI+AGF+AGY AR IS  L +P S+E+
Sbjct: 300 AGYIAWSIADRPGLAPGMIGGYLASTLGAGFLGGIIAGFLAGYVARFISQKLPMPESVES 359

Query: 358 LKPILVIPLLASLVTGLLMLYVVGKPVAGMLAALTGFLDGMGTSNAILLGLLLGGMMCVD 417
           LKPIL+IPLLASLVTGL M+YV+G+P A ++  LT FL+ MGT+NAILLG +LG MMC D
Sbjct: 360 LKPILIIPLLASLVTGLAMIYVIGEPAATLMDGLTNFLESMGTTNAILLGGILGAMMCFD 419

Query: 418 LGGPVNKAAYAFSVGLLS--SHSYAPMAAVMAAGMVPPIGMGLATLLARRKFAESERQAG 475
           LGGPVNKAAY F VGLLS  S   APMAA+MA+GMVP IGMG+A+ +A  KFAE+ERQAG
Sbjct: 420 LGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMASGMVPAIGMGVASFIAHTKFAEAERQAG 479

Query: 476 KAASVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLQAPHGGLFVMLV 535
           +A+ VLGLCFISEGAIPF AKDPLRVIP  + GGA+TGALSM F  KL APHGGLFV+ +
Sbjct: 480 RASFVLGLCFISEGAIPFMAKDPLRVIPVCMVGGAITGALSMLFTVKLMAPHGGLFVLAI 539

Query: 536 PNAINHALAYLLAIVAGSLLTGLLYAVLKRG 566
           PNA++  L Y+ AI  GSL+ G  YA++K G
Sbjct: 540 PNAVSAVLPYVAAIAIGSLVIGFGYAMIKTG 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: 894
Number of extensions: 44
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: 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 24 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