GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Pseudomonas fluorescens GW456-L13

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate PfGW456L13_3038 Multiple polyol-specific dehydrogenase (EC 1.1.1.-)

Query= BRENDA::Q9KWR5
         (485 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3038
          Length = 490

 Score =  357 bits (917), Expect = e-103
 Identities = 191/424 (45%), Positives = 260/424 (61%), Gaps = 4/424 (0%)

Query: 7   LKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHAP--DWAIVGVGLTG 64
           L  L   V  P Y +   + GI H GVG F RAH+A+Y + ++      DWAI GVGL  
Sbjct: 8   LNRLAPEVVLPAYALGETRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWAICGVGLRA 67

Query: 65  SDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLVDPAIR 124
            DR  +  ++ K QD L++L E   SG + VRV+GALRD LLA    +A++  L  P IR
Sbjct: 68  EDRRAR--DDLKDQDYLFTLFELGDSGDTEVRVIGALRDMLLAEDSAQALIDKLASPEIR 125

Query: 125 IVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAGGKAFT 184
           IVS+TITEGGY I+++TG F      ++ DL +P  P TVFG++  AL +R  AG  AFT
Sbjct: 126 IVSLTITEGGYCIDDSTGEFMAHLPQIQHDLAHPGAPKTVFGFLCAALAKRRAAGTAAFT 185

Query: 185 VMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEIAKKLN 244
           +MSCDNL HNG V RKA L +A   D +L  WI+ N +FPN MVDRITP  S     +L 
Sbjct: 186 LMSCDNLPHNGAVTRKALLAFAALHDSQLRDWIDTNVSFPNAMVDRITPMTSTLHRLQLA 245

Query: 245 AASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLNAGHVM 304
              G+DD  P+V E F QWVLED+F +GRP  EK GVQ   DVT +E +KI++LN  H+ 
Sbjct: 246 DRHGVDDAWPVVCEPFAQWVLEDRFVNGRPAWEKVGVQFTDDVTPYEEMKIKLLNGSHLA 305

Query: 305 LCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVISRFSNK 364
           L + G L GY  V +A+ D   +  ++ Y++ DV P L A  G+ L  Y++++++RFSN+
Sbjct: 306 LTYLGFLKGYRFVHEAMNDPLFVRYMRAYMDLDVTPQLPAVPGIDLAEYKNTLVARFSNQ 365

Query: 365 AMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEKGGTYE 424
           A++DQ  R+ SDG SK   F   T+ R I D  D  R A  +A++   L+G DE+G TY 
Sbjct: 366 AIADQLERVCSDGSSKFPKFTVPTINRLIADGCDTRRAALVVAAWALYLKGVDEQGETYT 425

Query: 425 SSEP 428
            ++P
Sbjct: 426 IADP 429


Lambda     K      H
   0.317    0.135    0.398 

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: 558
Number of extensions: 21
Number of successful extensions: 3
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: 485
Length of database: 490
Length adjustment: 34
Effective length of query: 451
Effective length of database: 456
Effective search space:   205656
Effective search space used:   205656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 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