GapMind for catabolism of small carbon sources

 

Alignments for a candidate for vorB in Geotalea uraniireducens Rf4

Align Ketoisovalerate oxidoreductase subunit VorB; VOR; 2-oxoisovalerate ferredoxin reductase subunit beta; 2-oxoisovalerate oxidoreductase beta chain; EC 1.2.7.7 (characterized)
to candidate WP_011939077.1 GURA_RS11115 2-oxoacid:acceptor oxidoreductase subunit alpha

Query= SwissProt::P80908
         (352 letters)



>NCBI__GCF_000016745.1:WP_011939077.1
          Length = 377

 Score =  221 bits (562), Expect = 3e-62
 Identities = 145/372 (38%), Positives = 205/372 (55%), Gaps = 34/372 (9%)

Query: 6   VKGNTAVIIGAMYAGCDCYFGYPITPASEILHEASRYFPLVGRKFVQAESEEAAINMVYG 65
           ++GN A   GA+YAGC  + GYPITP++E+    S   P +G KF+Q E E  A+  V G
Sbjct: 8   MQGNEAATHGALYAGCKFFAGYPITPSTEVAEVMSAELPKIGGKFIQMEDEIGAMAAVIG 67

Query: 66  AAAAGHRVMTASSGPGMSLKQEGISFLAGAELPAVIVDVMRAGPGLG-NIGPEQADYNQL 124
           A+ AG +V+T++SGPG+SLKQE I +   AE P VI++VMR GP  G   GP Q+D    
Sbjct: 68  ASLAGSKVLTSTSGPGLSLKQELIGYACIAETPCVIINVMRGGPSTGMPTGPSQSDV-MS 126

Query: 125 VKGGGHGNYRNIVLAPNSVQEMCDLTMDAFELADKYRNPVIILADAVLGQMAEPLRFPER 184
            K G HG++  I L P SVQE+ + T+ AF LA+KYR PV+++ D ++  M E + FPE+
Sbjct: 127 AKWGTHGDHPAICLVPASVQELFEETVRAFNLAEKYRTPVMVMPDEIVAHMRERIVFPEK 186

Query: 185 AVEHRPDTSWAVCGSRETMKNLVTSIFLDFDELEEF----NFYL--------------QE 226
                 D + A   S E  K   T  F D   L  F     F++                
Sbjct: 187 GELEVIDRT-APSVSPEQYKPYDTK-FGDVPPLAAFGSGYRFHVTGLNKAEDGFPTTKAS 244

Query: 227 KYAAVEENEVR-----------YEEYMVEDAEIVLVAYGISSRVAKSAVDTARADGIKVG 275
              A EE +VR           +EEYM++DAE+ +VA+G +SR A+ AV+ AR  GIK G
Sbjct: 245 LVQAEEERQVRKVDANVDDIVKFEEYMLDDAEVAIVAFGSTSRSARFAVNEARKQGIKAG 304

Query: 276 LLRPITLFPFPSERIRELAEGGCTFISVEMSSGQMREDI-KMASGCRDVELVNRMGGNLI 334
           L R  T +PFP ++++ LA     FI+ EM+ G    ++ + A G   V  + R+ G  I
Sbjct: 305 LFRIKTFWPFPDKQLKALASRVKAFITPEMNLGMCTVEVQRCAEGKAPVHGIFRVDGEPI 364

Query: 335 ELRDILRKIREI 346
               IL KI+E+
Sbjct: 365 NPGQILDKIKEV 376


Lambda     K      H
   0.319    0.136    0.390 

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: 302
Number of extensions: 13
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 352
Length of database: 377
Length adjustment: 29
Effective length of query: 323
Effective length of database: 348
Effective search space:   112404
Effective search space used:   112404
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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