GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo5_N2C3_1:AO356_07325
          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:

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