GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ydiJ in Azospirillum brasilense Sp245

Align D-2-hydroxyglutarate--pyruvate transhydrogenase DLD2; D-2HG--pyruvate transhydrogenase DLD2; Actin-interacting protein 2; D-lactate dehydrogenase [cytochrome] 2, mitochondrial; D-lactate ferricytochrome C oxidoreductase; D-LCR; EC 1.1.99.40; EC 1.1.2.4 (characterized)
to candidate AZOBR_RS29745 AZOBR_RS29745 2-hydroxyacid dehydrogenase

Query= SwissProt::P46681
         (530 letters)



>FitnessBrowser__azobra:AZOBR_RS29745
          Length = 467

 Score =  301 bits (771), Expect = 3e-86
 Identities = 169/459 (36%), Positives = 262/459 (57%), Gaps = 19/459 (4%)

Query: 82  SESEDLSFYNEDWMRKYKGQSKLVLRPKSVEKVSLILNYCNDEKIAVVPQGGNTGLVGGS 141
           ++ + +  + E W   + G+S  V+ P S E ++ ++  C + +  +VPQGGNTGL G S
Sbjct: 16  TDPDTMQPFMESWRDGWVGRSPAVVLPDSTEALAAVVRICAETRTPIVPQGGNTGLTGAS 75

Query: 142 VPIFD--ELILSLANLNKIRDFDPVSGILKCDAGVILENANNYVMEQNYMFPLDLGAKGS 199
            P  D  E++LS   LN+IR+ D  +  +  +AG IL N  N   +   +FP+ L A+GS
Sbjct: 76  QPHADGTEIVLSTNRLNRIREIDIDNDTMTVEAGCILANIQNAARDIGRLFPMSLAAEGS 135

Query: 200 CHVGGVVATNAGGLRLLRYGSLHGSVLGLEVVMPNGQIVNSMHSMRKDNTGYDLKQLFIG 259
           C +GG +ATNAGG++++RYG++   V GLEVV+P+G+I + +  +RKDN GYD+KQ+FIG
Sbjct: 136 CQIGGNIATNAGGVQVVRYGNMRNLVAGLEVVLPDGRIWDGLRGLRKDNAGYDMKQIFIG 195

Query: 260 SEGTIGIITGVSILTVPKPKAFNVSYLSVESFEDVQKVFVRARQELSEILSAFEFMDAKS 319
           SEGT+GI+T   +   P P+A   + ++V +  D   +  RA+    + +  FE +    
Sbjct: 196 SEGTLGIVTAAVLKLSPLPRATATALVAVSAPSDAVDLLTRAKGVAGDRIITFELIQRDC 255

Query: 320 QVLAKSQLKDAAFPLEDEHPFYILIETS---GSNKDHDDSKLETFLENVMEEGIVTDGVV 376
             +A+  + D   PL D +P+Y+L+E +   G N+  +   LE  LE  ME G V DGVV
Sbjct: 256 IDVARRHVPDVPDPLRDRYPWYVLVELADQDGGNRLME--MLEGILEAGMEAGEVLDGVV 313

Query: 377 AQDETELQNLWKWREMIPEASQANGGVYKYDVSLPLKDLYSLVEATNARLSEAELVGDSP 436
           A  + +  +LW+ RE IPE  +  G  +K+DVS+P+  +   ++  NA L E E  G  P
Sbjct: 314 AASKAQADSLWRIREGIPEGQKREGVSFKHDVSVPISRVARFLDRANAAL-ERECPGIRP 372

Query: 437 KPVVGAIGYGHVGDGNLHLNVAVREYNKNIE-----KTLEPFVYEFVSSKHGSVSAEHGL 491
                   +GH+GDGN+H N    E     E      T+   V++ V    GS+SAEHG+
Sbjct: 373 ------FAFGHLGDGNIHFNPIQAEGGDPAEWKAKLATVNAIVHDIVVELGGSISAEHGI 426

Query: 492 GFQKKNYIGYSKSPEEVKMMKDLKVHYDPNGILNPYKYI 530
           G  + + +   KS  E+ MM  LK  +DP+ I+NP K +
Sbjct: 427 GRLRIDEMPRYKSAVELDMMATLKRAFDPHNIMNPGKIL 465


Lambda     K      H
   0.316    0.135    0.385 

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: 523
Number of extensions: 18
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: 530
Length of database: 467
Length adjustment: 34
Effective length of query: 496
Effective length of database: 433
Effective search space:   214768
Effective search space used:   214768
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:

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