Alignments for a candidate for fruII-ABC in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruII-ABC in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_5073 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)

Query= TCDB::P71012
         (635 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5073
          Length = 579

 Score =  443 bits (1140), Expect = e-129
 Identities = 235/516 (45%), Positives = 340/516 (65%), Gaps = 26/516 (5%)

Query: 125 MREEIRKQLLEAESEDAIIDI--INQHDKDDDEEEEEEEAAPAPAG----KGKILAVTAC 178
           M   + K++ ++    A+ D+  + +    D +    EEAA  P        +++AVTAC
Sbjct: 69  MSRFVGKRVFQSTPAQALQDVEAVLRRGAQDAQVYAAEEAAVEPVAVVQNAPRLVAVTAC 128

Query: 179 PTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADKQVEM 238
           PTG+AHTFMAA+AL++ AK LG E++VET GS G ++ L+AQ I +A  +++AAD +V  
Sbjct: 129 PTGVAHTFMAAEALQQAAKRLGYELQVETQGSVGARNPLSAQAIAEADVVLLAADIEVAT 188

Query: 239 ERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAKGKSGSGIG 298
           ERF GK++ +      +++ +  ++KA+ +     Q S   +A +   +E  G       
Sbjct: 189 ERFAGKKIYRCGTGIALKQAEATLKKALAEGQ---QESASSAAKTTAKQEKTG------- 238

Query: 299 NTFYKHLMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNFIGGDNALK 358
              YKHL++GVS MLP VV GG+++A+SF +GI +         T AAAL  IGGD+A K
Sbjct: 239 --VYKHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEE----GTLAAALMQIGGDSAFK 292

Query: 359 LIVAVLAGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVILLKKVFTF 418
           L+V +LAG+IA SIADRPG APGM+GG +A+   AGF+GG+IAGFLAGY    + + +  
Sbjct: 293 LMVPLLAGYIAYSIADRPGLAPGMIGGLLASTLGAGFIGGIIAGFLAGYAARAINR-YAR 351

Query: 419 IPQSLDGLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGNLVLMGIIL 478
           +PQSL+ LKP+LI PL     TG++M +VV  PVA  +  LTN+L+S+GT N +L+G++L
Sbjct: 352 LPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAGMLAGLTNFLDSMGTTNAILLGVLL 411

Query: 479 GGMMAIDMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIALATTIFRNKFTQR 538
           GGMM +D+GGP+NKAA+ F + ++ + +YAP AA MA GMVPP+G+ +AT I R KF Q 
Sbjct: 412 GGMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATFIARRKFAQT 471

Query: 539 DREAGITCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRVTLPAPHGGV 598
           +REAG     +G  F++EGAIPFAA DPLRVIPA++ G A+ G L+ +F   L APHGG+
Sbjct: 472 EREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMAPHGGL 531

Query: 599 FVAFI---TNHPMLYLLSIVIGAVVMAIILGIVKKP 631
           FV  I    NH +LYLL+IV G+++ A+   +VK+P
Sbjct: 532 FVLAIPNAINHALLYLLAIVAGSLLTAVAYALVKRP 567



 Score = 52.8 bits (125), Expect = 4e-11
 Identities = 30/103 (29%), Positives = 52/103 (50%), Gaps = 1/103 (0%)

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

Query: 231 AADKQVEMERFKGKRVLQVPVTAGIRRPQELIEKAMNQDAPIY 273
                VEM RF GKRV Q      ++  + ++ +   QDA +Y
Sbjct: 62  VTSAPVEMSRFVGKRVFQSTPAQALQDVEAVLRRGA-QDAQVY 103


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: 793
Number of extensions: 32
Number of successful extensions: 6
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: 579
Length adjustment: 37
Effective length of query: 598
Effective length of database: 542
Effective search space:   324116
Effective search space used:   324116
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
the source code
instructions for running GapMind on your computer

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