Aligments for a candidate for fruII-ABC in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruII-ABC in Pseudomonas fluorescens FW300-N2C3

Align The fructose porter, FruA (fructose-1-P forming IIABC) (Delobbe et al. 1975) FruA is 39% identical to 4.A.2.1.1). fructose can be metabolized to Fru-1-P via this system as well as Fru-6-P by another PTS system (characterized)
to candidate AO356_07325 AO356_07325 PTS fructose transporter subunit IIBC

Query= TCDB::P71012
         (635 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_07325 AO356_07325 PTS
           fructose transporter subunit IIBC
          Length = 580

 Score =  430 bits (1106), Expect = e-125
 Identities = 220/481 (45%), Positives = 326/481 (67%), Gaps = 24/481 (4%)

Query: 158 EEEEAAPAPAGKG----KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGI 213
           E + +A  PA       +++A+TACPTG+AHTFMAA+AL++ A +LG +++VET GS G 
Sbjct: 105 EADASAQVPAASAERAPRLVAITACPTGVAHTFMAAEALQQAATKLGYDLQVETQGSVGA 164

Query: 214 KHKLTAQEIEDAPAIIVAADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIY 273
           ++ L+A+ I +A  +++A D +V  ERF GK++ +      +++ +  + KA+ +     
Sbjct: 165 RNPLSAEAIAEADVVLLATDIEVATERFAGKKIYRCGTGIALKQAEATLNKALVEARQES 224

Query: 274 QGSGGGSAASNDDEEAKGKSGSGIGNTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHS 333
             SG  + A ++      K+G+      YKHL++GVS MLP VV GG+++A+SF +GI +
Sbjct: 225 ASSGASAPAKSE------KTGA------YKHLLTGVSFMLPMVVAGGLMIALSFVFGIEA 272

Query: 334 ADPNDPSYNTFAAALNFIGGDNALKLIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANA 393
               +P   T AAAL  IGG+ A KL+V +LAG+IA SIADRPG APGM+GG +A+   A
Sbjct: 273 F--KEPG--TLAAALMQIGGETAFKLMVPLLAGYIAYSIADRPGLAPGMIGGMLASTLGA 328

Query: 394 GFLGGLIAGFLAGYVVILLKKVFTFIPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVA 453
           GF+GG+IAGFLAGY    + + +  +PQSL+ LKP+LI PL     TG++M ++V  PVA
Sbjct: 329 GFIGGIIAGFLAGYAAKAISR-YARLPQSLEALKPILIIPLLASLFTGLVMIYIVGKPVA 387

Query: 454 AFMNFLTNWLESLGTGNLVLMGIILGGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAI 513
             +  LT++L+S+GT N +L+G++LG MM +D+GGP+NKAA+ F + ++ + +YAP AA 
Sbjct: 388 GMLEALTHFLDSMGTTNAILLGVLLGAMMCVDLGGPINKAAYAFSVGLLASQSYAPMAAA 447

Query: 514 MAGGMVPPLGIALATTIFRNKFTQRDREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAA 573
           MA GMVPP+G+ +AT I R KF Q +REAG     +G  F++EGAIPFAA DPLRVIPA+
Sbjct: 448 MAAGMVPPIGLGIATFIARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPAS 507

Query: 574 VVGAAVAGGLTEFFRVTLPAPHGGVFVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKK 630
           + G A+ G L+ +F   L APHGG+FV  I    NH +LYLL+IV G+++ A+   ++K+
Sbjct: 508 IAGGALTGALSMYFGCKLMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTAVAYALLKR 567

Query: 631 P 631
           P
Sbjct: 568 P 568



 Score = 48.1 bits (113), Expect = 1e-09
 Identities = 25/78 (32%), Positives = 43/78 (55%)

Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230
           K+  VTACP G+  + + A  L   A+  G    VE + ++  + +L+A  +E A  +++
Sbjct: 2   KLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEAAEWVLL 61

Query: 231 AADKQVEMERFKGKRVLQ 248
            A   V++ RF GKRV +
Sbjct: 62  VASGPVDLSRFVGKRVFR 79


Lambda     K      H
   0.320    0.137    0.390 

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: 765
Number of extensions: 33
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: 635
Length of database: 580
Length adjustment: 37
Effective length of query: 598
Effective length of database: 543
Effective search space:   324714
Effective search space used:   324714
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 (21.8 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources