Aligments for a candidate for lctD in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for lctD in Phaeobacter inhibens BS107

Align lactate dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.110) (characterized)
to candidate GFF2781 PGA1_c28240 putative D-lactate dehydrogenase

Query= BRENDA::H6LBS1
         (466 letters)



>FitnessBrowser__Phaeo:GFF2781
          Length = 467

 Score =  226 bits (576), Expect = 1e-63
 Identities = 147/453 (32%), Positives = 234/453 (51%), Gaps = 19/453 (4%)

Query: 21  ERVFVGTEIGEDFSHDELGSIHSYPEVLIKVTSTEEVSKIMKYAYEHNIPVVVRGSGTGL 80
           E++  G  I E   H      +  P+ ++  TST+EV+ I++   ++ +PV+  G+GT L
Sbjct: 27  EQLQTGQAIREQHGHTTTWITNQPPDAVVFPTSTDEVADIVRTCADYGVPVIPYGTGTSL 86

Query: 81  VGACVPLFGGIMLETTLMNNILELDTENLTVTVEPGVLLMELSKFVEENDLFYPPDPGEK 140
            G      GGI ++   M+ IL +  E+L V V+PGV   +L+ ++ +  LF+P DPG  
Sbjct: 87  EGHVNAPAGGICVDMMRMDKILAVHAEDLDVVVQPGVTREQLNTYLRDQGLFFPIDPGA- 145

Query: 141 SATIAGNISTNAGGMRAVKYGVTRDYVRGLTVVLANGEIIELGGKIVKNSSGYSLKDLVI 200
           +A++ G  +T A G  AV+YG  +D V  L  V+A+G +I    +  K+S+GY +  L++
Sbjct: 146 NASLGGMAATRASGTNAVRYGTMKDNVLALEAVMADGGVIRTAQRAKKSSAGYDMTRLLV 205

Query: 201 GSEGTLCVITKAILKLLPLPKMTLSLLIPFENISDAAGIVPKIIKSKAIPTAIEFMERQT 260
           GSEGTL +IT+  L+L  +P+   S    F ++ DA   V   I+     + IE ++  +
Sbjct: 206 GSEGTLGLITELTLRLQGIPEAIRSARCAFRSVDDACRAVMMTIQYGIPVSRIELLDEMS 265

Query: 261 ILFAEDFLGKKFPDSSSNAYILLTFDGNTKEQVEAEYETVANLCLAEGAKDVYIVDTVER 320
           +  A  + G   P+      +LL F G+    VE + +T A +    G  D+    T E 
Sbjct: 266 VRAANAYSGLDLPEM---PLLLLEFHGSDAGVVE-QADTFAQIAEEFGGFDIAATSTAEE 321

Query: 321 KDSVWSARGAFLEA---IKASTTEMDECDVVVPRNRIAEFIEFTHDLAKEMDVRIPSFGH 377
           +  +W AR     A   ++     +   DV VP +++AE +      A+EM++  P  GH
Sbjct: 322 RSKLWQARHDMYWASLQLRPGAKGI-STDVCVPISKLAECVSAARSKAEEMNLLAPMVGH 380

Query: 378 AGDGNLHIYVCRDELCQADWEAKLAEAMDR----MYAKALTFEGLVSGEHGIGYAKRKYL 433
            GDGN H  +    L   D  A+  EA D     +   A++ EG  +GEHGIG  KR YL
Sbjct: 381 VGDGNFHALL----LINMD-SAEEREAADAYVGWLNELAISIEGTCTGEHGIGQGKRPYL 435

Query: 434 LNDFGTEHLALMAGIKQTFDPKNLLNPKKVCQM 466
             + G E    MA IK   DP+N+LNP K+ ++
Sbjct: 436 QQELG-ETTRYMAAIKAALDPENILNPGKILEI 467


Lambda     K      H
   0.318    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: 474
Number of extensions: 19
Number of successful extensions: 5
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: 466
Length of database: 467
Length adjustment: 33
Effective length of query: 433
Effective length of database: 434
Effective search space:   187922
Effective search space used:   187922
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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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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, 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

GapMind for catabolism of small carbon sources