GapMind for catabolism of small carbon sources

 

Alignments for a candidate for vorA in Desulfovibrio vulgaris Hildenborough

Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate 208875 DVU3348 pyruvate ferredoxin/flavodoxin oxidoreductase, beta subunit, putative

Query= SwissProt::P80907
         (478 letters)



>MicrobesOnline__882:208875
          Length = 260

 Score =  251 bits (640), Expect = 3e-71
 Identities = 118/229 (51%), Positives = 156/229 (68%)

Query: 26  ATHYCAGCGHGILHKLIGEAIDELGIQERSVMISPVGCAVFAYYYFDCGNVQVAHGRAPA 85
           ATHYC GC HG+ H+L+ E + E+G+ E ++ +S +GC+VF Y Y     V+  HGRAPA
Sbjct: 24  ATHYCPGCHHGVAHRLVAEVLTEMGVAEDTICVSSIGCSVFIYNYLAVDTVEAPHGRAPA 83

Query: 86  VGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAANRGEKMAVFFVNNTVYGMTGGQMAP 145
           V TG+ RA    +V  YQGDGDLASIGL E + AANRGE+M + FVNNTVYGMTGGQMAP
Sbjct: 84  VATGVKRARKDKIVFAYQGDGDLASIGLAEIMHAANRGERMTIVFVNNTVYGMTGGQMAP 143

Query: 146 TTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQAPVFIERVSLADPKSIRKAKRAVKRA 205
           TTL+G+ T TCP GR     G P+ M E++  L    +  RVSL   K IR AK+A+++A
Sbjct: 144 TTLVGQKTTTCPSGRCRDTEGLPMKMAEIIAGLGGVAYSARVSLDSVKHIRAAKKALRKA 203

Query: 206 LEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLKEEMEREFPVKNFRD 254
            ++Q++  G+ FVE+LS CPTN R DA  A + + EEM   FP+  ++D
Sbjct: 204 FDVQQNDLGFGFVEMLSACPTNWRMDAVKANKRIAEEMIPYFPLGVYKD 252


Lambda     K      H
   0.318    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: 320
Number of extensions: 14
Number of successful extensions: 1
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: 478
Length of database: 260
Length adjustment: 29
Effective length of query: 449
Effective length of database: 231
Effective search space:   103719
Effective search space used:   103719
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: 49 (23.5 bits)

Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate 208874 DVU3347 pyruvate ferredoxin/flavodoxin oxidoreductase family protein

Query= SwissProt::P80907
         (478 letters)



>MicrobesOnline__882:208874
          Length = 182

 Score =  124 bits (312), Expect = 2e-33
 Identities = 75/178 (42%), Positives = 104/178 (58%), Gaps = 7/178 (3%)

Query: 299 VKIAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAV 358
           V +AGFGGQGV+ +G  LA A    G + ++ P YGPE RGGT++C VV+S E +GSP +
Sbjct: 7   VIMAGFGGQGVMLIGNLLAYAGMHAGLNVTYIPVYGPEMRGGTANCTVVVSDEDIGSPII 66

Query: 359 DTPDVLVAFNQPSLDEFAGDVREGGIVLYDTATADFSKKE-NLRAIGVPALEIAKEHGTG 417
             P  L+  NQPSLD+F   + +GG+ + +T+  D SK E  +R + VPA EIA   G  
Sbjct: 67  QRPKSLIIMNQPSLDKFEARLEDGGVQVLNTSLVDASKAEARVRTVCVPANEIADGIGNT 126

Query: 418 RAANTAMLGV-MMALGITGLD--EESFRDAIRFTFSGKDKIIDINLKILEAGADWARK 472
           + AN   LG  + A GI  L+  +ES +  I   +S    +I  N   L+AG D A K
Sbjct: 127 KMANMVALGAYVQATGIVPLEAVKESLKSVISAHYS---HLIPKNADALQAGFDHAAK 181


Lambda     K      H
   0.318    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: 182
Number of extensions: 10
Number of successful extensions: 2
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: 478
Length of database: 182
Length adjustment: 26
Effective length of query: 452
Effective length of database: 156
Effective search space:    70512
Effective search space used:    70512
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: 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