Alignments for a candidate for fruII-ABC in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruII-ABC in Pseudomonas simiae WCS417

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 GFF782 PS417_03975 FruA

Query= TCDB::P71012
         (635 letters)



>FitnessBrowser__WCS417:GFF782
          Length = 569

 Score =  423 bits (1088), Expect = e-123
 Identities = 227/514 (44%), Positives = 331/514 (64%), Gaps = 23/514 (4%)

Query: 125 MREEIRKQLLEAESEDAIIDIINQHDKDDDEEEEEEEAAPAPAGKGKILAVTACPTGIAH 184
           M+  + K++ ++    A+ D+     +  +E +       A     +I+A+TACPTG+AH
Sbjct: 69  MQRFVGKRVFQSTPAQALADVDAVLRRGAEEAQVYVATQQAAENAPRIVAITACPTGVAH 128

Query: 185 TFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIVAADKQVEMERFKGK 244
           TFMAA+AL++ AK LG +++VET GS G +  L+ Q I +A  +++AAD +V  ERF GK
Sbjct: 129 TFMAAEALQQTAKRLGYDLQVETQGSVGARTPLSPQAIAEADVVLLAADIEVATERFAGK 188

Query: 245 RVLQVPVTAGIRRPQELIEKAMNQDAPIYQGSGGGSAASNDDEEAKGKSGSGIGNTFYKH 304
           ++ +      +++ +  + KA+ + A   + +  G+ A       K K+G       YKH
Sbjct: 189 KIYRCGTGIALKQSEATLNKALAEGA--VESAASGAVAK------KEKTG------VYKH 234

Query: 305 LMSGVSNMLPFVVGGGILVAISFFWGIHSADPNDPSYNTFAAALNFIGGDNALKLIVAVL 364
           L++GVS MLP VV GG+L+A+SF +GI + +       T AAAL  +G D A  L+V +L
Sbjct: 235 LLTGVSFMLPMVVAGGLLIALSFMFGITAFEEK----GTLAAALKTVG-DQAFMLMVPLL 289

Query: 365 AGFIAMSIADRPGFAPGMVGGFMATQANAGFLGGLIAGFLAGYVVILLKKVFTFIPQSLD 424
           AG+IA SIADRP  APGM+GG +AT   AGF+GG+ AGFLAGY V L+ +    +PQSLD
Sbjct: 290 AGYIAYSIADRPALAPGMIGGLLATTLGAGFIGGIFAGFLAGYCVKLITRAVQ-LPQSLD 348

Query: 425 GLKPVLIYPLFGIFITGVLMQFVVNTPVAAFMNFLTNWLESLGTGNLVLMGIILGGMMAI 484
            LKP+LI PL     TG+ M ++V  PVA  +  LT +L ++GT N VL+GI+LGGMM +
Sbjct: 349 ALKPILIIPLLASLFTGLAMIYLVGPPVARMLVGLTEFLNTMGTTNAVLLGILLGGMMCV 408

Query: 485 DMGGPLNKAAFTFGIAMIDAGNYAPHAAIMAGGMVPPLGIALATTIFRNKFTQRDREAGI 544
           D+GGP+NKAA+ F + M+ A + AP AA MA GMVPP+G+ +AT + R KF Q +REAG 
Sbjct: 409 DLGGPINKAAYAFSVGMLAAHSGAPIAATMAAGMVPPIGMGIATFLARRKFAQTEREAGK 468

Query: 545 TCYFMGAAFVTEGAIPFAAADPLRVIPAAVVGAAVAGGLTEFFRVTLPAPHGGVFVAFI- 603
               +G  F++EGAIPFAA DPLRVIPA++ G A+AG L+ +F   L APHGG+ V  I 
Sbjct: 469 AAIILGMVFISEGAIPFAAKDPLRVIPASIAGGALAGALSMYFGCKLAAPHGGLAVLVIP 528

Query: 604 --TNHPMLYLLSIVIGAVVMAIILGIVKKPVTEK 635
              NH +LYLL+IV G+++  ++  ++K+P  ++
Sbjct: 529 NAMNHALLYLLAIVAGSLLTGLVYALIKRPEAQE 562



 Score = 48.5 bits (114), Expect = 8e-10
 Identities = 26/78 (33%), Positives = 41/78 (52%)

Query: 171 KILAVTACPTGIAHTFMAADALKEKAKELGVEIKVETNGSSGIKHKLTAQEIEDAPAIIV 230
           K+  VTACP G+  + + A  L   A+  G    VE       + +L+   I+DA  +++
Sbjct: 2   KLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDVQRPERQLSQATIDDAEWVLL 61

Query: 231 AADKQVEMERFKGKRVLQ 248
            +   V+M+RF GKRV Q
Sbjct: 62  VSSTPVDMQRFVGKRVFQ 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: 810
Number of extensions: 36
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: 569
Length adjustment: 37
Effective length of query: 598
Effective length of database: 532
Effective search space:   318136
Effective search space used:   318136
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