GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Pseudomonas stutzeri RCH2

Align D-lactate dehydrogenase (acceptor) (EC 1.1.99.6) (characterized)
to candidate GFF3772 Psest_3841 glycolate oxidase, subunit GlcD

Query= BRENDA::O29853
         (443 letters)



>FitnessBrowser__psRCH2:GFF3772
          Length = 499

 Score =  196 bits (499), Expect = 1e-54
 Identities = 130/422 (30%), Positives = 223/422 (52%), Gaps = 20/422 (4%)

Query: 38  VVVKPSNSEEVSAILKFANEKSIPVFMRGGGTGLSGGAVPTEEGIVLSTEKMTE-LEVDA 96
           +VV P   E+V  +LK  +++ +PV  RG GTGLSGGA+P E+GI+L   +  + LEVD 
Sbjct: 58  LVVLPERIEQVETLLKLCHQRGVPVVARGAGTGLSGGALPLEQGILLVMARFNKILEVDP 117

Query: 97  DNRVAICGAGVTLKQLDDAAFRHGLSFPPHPGAETA-TVGGMIATNAGGVRALKYGTMRN 155
             R A    GV    +  AA  + L + P P ++ A ++GG +A NAGGV  LKYG   +
Sbjct: 118 AGRFARVQPGVRNLAISQAAAPYELYYAPDPSSQIACSIGGNVAENAGGVHCLKYGLTVH 177

Query: 156 YVLSLEAVLADGRIINVGGKTIKNSSGYSLLHLLVGSEGTLAVITKATIRLFPQMRDMTV 215
            +L ++ +  +G  + +G   + +S G+ LL L  GSEG L ++T+ T++L P+ +   V
Sbjct: 178 NLLKVDILTVEGERMTLGSDAL-DSPGFDLLALFTGSEGMLGIVTEVTVKLLPKPQVAKV 236

Query: 216 LAIPFPTMEDAMNCVVE-VARKMLPMALEFMEKRAVEIGEKVSGERWVSREGEAHLLMVF 274
           L   F ++E A   V + +A  ++P  LE M+  ++   E      +   + EA LL   
Sbjct: 237 LLAAFDSVEKAGRAVGDIIAAGIIPGGLEMMDNLSIRAAEDFIHAGY-PVDAEAILLCEL 295

Query: 275 ES-----FDEAEEAAKIAQSLGAIDVYAATTKKDQDRLLKVRGMIYEGLRKEVIE--VLD 327
           +       D+    +++ +  GA +V  A  + ++ R    R   +  + +   +   +D
Sbjct: 296 DGVEADVHDDCARVSEVLKLAGATEVRLAKDEAERVRFWAGRKNAFPAVGRISPDYYCMD 355

Query: 328 ACVPPAKIAEYWRRSNELAEEYGIELITYGHAGDGNVHQHPLV-YEGWEKSYFEFRKSL- 385
             +P  ++    +  ++L+E++G+ +    HAGDGN+  HPL+ ++  +    E  + L 
Sbjct: 356 GTIPRRELPGVLKGISDLSEQFGLRVANVFHAGDGNM--HPLILFDANQPGELERAEDLG 413

Query: 386 ---LSLAVSLGGVISGEHGIGAVKLSELEELF-PEQFELMRQIKLLFDPKNILNPGKVVR 441
              L L V +GG I+GEHG+G  K++++   F  ++  L   +K  FDP  +LNPGK + 
Sbjct: 414 GKILELCVKVGGSITGEHGVGREKINQMCSQFNADELTLFHAVKAAFDPSGLLNPGKNIP 473

Query: 442 KL 443
            L
Sbjct: 474 TL 475


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: 491
Number of extensions: 23
Number of successful extensions: 6
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: 499
Length adjustment: 33
Effective length of query: 410
Effective length of database: 466
Effective search space:   191060
Effective search space used:   191060
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:

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