GapMind for catabolism of small carbon sources

 

Aligments for a candidate for sdh in Pseudomonas fluorescens FW300-N2E3

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate AO353_25900 AO353_25900 mannitol dehydrogenase

Query= BRENDA::Q9KWR5
         (485 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_25900 AO353_25900 mannitol
           dehydrogenase
          Length = 491

 Score =  356 bits (913), Expect = e-102
 Identities = 186/429 (43%), Positives = 259/429 (60%), Gaps = 4/429 (0%)

Query: 2   ITRETLKSLPANVQAPPYDIDGIKPGIVHFGVGNFFRAHEAFYVEQILEHAP--DWAIVG 59
           + +  L  L   V  P Y +   + GI H GVG F RAH+A+Y + ++      DW+I G
Sbjct: 3   LNKPNLTRLAPEVALPAYTLSATRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSICG 62

Query: 60  VGLTGSDRSKKKAEEFKAQDCLYSLTETAPSGKSTVRVMGALRDYLLAPADPEAVLKHLV 119
           +GL   DR  +  ++  +QD L++L E   SG + VRV+GA+ D LLA  D +A++  L 
Sbjct: 63  IGLRAEDRRAR--DDLASQDYLFTLFELGDSGDTEVRVIGAISDMLLAEDDTQALIDKLA 120

Query: 120 DPAIRIVSMTITEGGYNINETTGAFDLENAAVKADLKNPEKPSTVFGYVVEALRRRWDAG 179
            P IRIVS+TITEGGY I+++TG F  +   ++ DL +P  P TVFG++  AL +R  AG
Sbjct: 121 SPDIRIVSLTITEGGYCIDDSTGEFMAQLPQIQHDLAHPNAPKTVFGFLCAALAKRRAAG 180

Query: 180 GKAFTVMSCDNLRHNGNVARKAFLGYAKARDPELAKWIEENATFPNGMVDRITPTVSAEI 239
             AFT+MSCDNL HNG V RKA L +A  RD +L  WI  N +FPN MVDRITP  S+  
Sbjct: 181 IPAFTLMSCDNLPHNGAVTRKALLAFAALRDADLRDWIGANVSFPNAMVDRITPMTSSAH 240

Query: 240 AKKLNAASGLDDDLPLVAEDFHQWVLEDQFADGRPPLEKAGVQMVGDVTDWEYVKIRMLN 299
              L+   G+DD  P+V E F QWVLED F +GRP  EK GVQ   DVT +E +KI++LN
Sbjct: 241 RLHLHDEHGIDDLWPVVCEPFVQWVLEDNFVNGRPAWEKVGVQFTDDVTPYEEMKIKLLN 300

Query: 300 AGHVMLCFPGILVGYENVDDAIEDSELLGNLKNYLNKDVIPTLKAPSGMTLEGYRDSVIS 359
             H+ L + G L GY  V + + D   +  ++ Y++ DV P L    G+ L  Y+++++ 
Sbjct: 301 GSHLALTYLGFLKGYRFVHETMNDPLFVRYMRAYMDLDVTPQLAPVPGIDLTQYKNTLVE 360

Query: 360 RFSNKAMSDQTLRIASDGCSKVQVFWTETVRRAIEDKRDLSRIAFGIASYLEMLRGRDEK 419
           RFSN+A++DQ  R+ SDG SK   F   T+ R I D R+  R A  +A++   L+G DE 
Sbjct: 361 RFSNQAIADQLARVCSDGSSKFPKFTVPTINRLIADGRETKRAALVVAAWAIYLKGVDEN 420

Query: 420 GGTYESSEP 428
           G TY   +P
Sbjct: 421 GDTYPIPDP 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: 570
Number of extensions: 19
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: 491
Length adjustment: 34
Effective length of query: 451
Effective length of database: 457
Effective search space:   206107
Effective search space used:   206107
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 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