GapMind for catabolism of small carbon sources

 

Aligments for a candidate for D-LDH in Pseudomonas fluorescens FW300-N2E2

Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate Pf6N2E2_137 Glycolate dehydrogenase (EC 1.1.99.14), subunit GlcD

Query= BRENDA::O29853
         (443 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_137 Glycolate
           dehydrogenase (EC 1.1.99.14), subunit GlcD
          Length = 511

 Score =  203 bits (517), Expect = 9e-57
 Identities = 137/422 (32%), Positives = 219/422 (51%), Gaps = 20/422 (4%)

Query: 38  VVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIVLSTEKMTE-LEVDA 96
           +V  P   E+V A+LK  +   +PV  RG GTGLSGGA+P E G++L   +  + L +D 
Sbjct: 70  LVALPRRVEQVQALLKLCHGLDVPVVARGAGTGLSGGALPLESGVLLVMARFNQILHIDP 129

Query: 97  DNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATNAGGVRALKYGTMRN 155
           D R A    GV    +  AA   GL + P P ++ A ++GG +A NAGGV  LKYG   +
Sbjct: 130 DARTARLQPGVRNLAISQAAAPFGLYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVH 189

Query: 156 YVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITKATIRLFPQMRDMTV 215
            +L LE +  +G  + +G + + +S G  LL L  GSEG L VIT+ T++L P+ +   V
Sbjct: 190 NLLKLEILTIEGERLTLGSEAL-DSPGLDLLALFTGSEGLLGVITEVTVKLLPRPQVAKV 248

Query: 216 LAIPFPTMEDAMNCVVE-VARKMLPMALEFMEKRAVEIGEKVSGERWVSREGEAHLLMVF 274
           L   F +++ A   V + +A  ++P  LE M+  A+   E      +   E EA LL   
Sbjct: 249 LLASFDSVDKAGRAVADIIAAGIIPGGLEMMDNLAIRAAEDFIHAGY-PVEAEAILLCEL 307

Query: 275 ES-----FDEAEEAAKIAQSLGAIDVYAATTKKDQDRLLKVRGMIYEGLRKEVIE--VLD 327
           +       D+ E   ++ +  GA +V  A  + ++ R    R   +  + +   +   +D
Sbjct: 308 DGVEADVHDDCERVRQVLEQAGATEVRQARDEAERLRFWAGRKNAFPAVGRLAPDYYCMD 367

Query: 328 ACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLV-YEGWEKSYFEFRKSL- 385
             +P   + E  +R   L  E+G+ +    HAGDGN+  HPL+ ++  +    E  ++L 
Sbjct: 368 GTIPRRALPEVLQRIASLGAEHGLRVANVFHAGDGNM--HPLILFDANQPGELERAETLG 425

Query: 386 ---LSLAVSLGGVISGEHGIGAVKLSELEELF-PEQFELMRQIKLLFDPKNILNPGKVVR 441
              L L V +GG I+GEHG+G  K++++   F  ++  L   +K  FDP+ +LNPGK + 
Sbjct: 426 GKILELCVQVGGSITGEHGVGREKINQMCTQFNSDELNLFHAVKAAFDPQGLLNPGKNIP 485

Query: 442 KL 443
            L
Sbjct: 486 TL 487


Lambda     K      H
   0.317    0.136    0.388 

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: 498
Number of extensions: 25
Number of successful extensions: 7
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: 443
Length of database: 511
Length adjustment: 33
Effective length of query: 410
Effective length of database: 478
Effective search space:   195980
Effective search space used:   195980
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 (21.7 bits)
S2: 51 (24.3 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