GapMind for catabolism of small carbon sources

 

Alignments for a candidate for D-LDH in Pseudomonas fluorescens FW300-N2E3

Align D-lactate dehydrogenase (EC 1.1.1.28) (characterized)
to candidate AO353_23780 AO353_23780 hydroxyacid dehydrogenase

Query= BRENDA::Q9I530
         (329 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_23780
          Length = 317

 Score =  129 bits (323), Expect = 1e-34
 Identities = 97/287 (33%), Positives = 140/287 (48%), Gaps = 32/287 (11%)

Query: 43  QGFEVVCAFVNDDL-------SRPVLERLAAGGTRLVALRSAGYNHVDLAAAEALGLPVV 95
           Q FEV+C      L       + P L+ L  GG R  A        +DL AA ALG+ V 
Sbjct: 48  QSFEVICVMRERTLFDEALLRNLPKLKLLVTGGMRNAA--------IDLKAAAALGIQVC 99

Query: 96  HVPAYSPHAVAEHAVGLILTLNRRLHRAYNRTREGDFSLHGLTGFDLHGKRVGVIGTGQI 155
              +Y   A  E    LI+ L R L    N  R G +   GL G DL+GK +G++G G I
Sbjct: 100 GTDSYK-QAAPELTWTLIMALTRNLLAEANALRAGHWQ-QGLGG-DLYGKTLGILGLGSI 156

Query: 156 GETFARIMAGFGCELLAY-DPYPNPRIQALGGRYLALDALLAESDIVSLHCPLTADTRHL 214
           G+  A     FG  ++A+ +     R    G  +++   L  ++D++S+H  L+  +R L
Sbjct: 157 GKRIAEFGQVFGMRVIAWSENLTAERAAEAGVTFVSKRELFEQADVLSIHLVLSERSRGL 216

Query: 215 IDAQRLATMKPGAMLINTGRGALVNAAALIEALKSGQLGYLGLDVYEEEADIFFEDRSDQ 274
           +D Q L  MKP A+LINT RG +V+ AALI+AL+  +L    LDV+E E           
Sbjct: 217 VDEQALGWMKPSALLINTARGPIVDEAALIQALEQNRLKGAALDVFERE----------- 265

Query: 275 PLQDDVLARLLSFPNVVVTAHQAFLTREALAAIADTTLDNIAAWQDG 321
           PL  D   R L  PNV+ T H  +++ +         +++I AW  G
Sbjct: 266 PLAADHPFRTL--PNVLATPHVGYVSEQNYRLFFSQMIEDIQAWTTG 310


Lambda     K      H
   0.323    0.137    0.402 

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: 248
Number of extensions: 18
Number of successful extensions: 4
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: 329
Length of database: 317
Length adjustment: 28
Effective length of query: 301
Effective length of database: 289
Effective search space:    86989
Effective search space used:    86989
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 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