GapMind for catabolism of small carbon sources

 

Alignments for a candidate for vorA in Methanobacterium arcticum M2

Align Ketoisovalerate oxidoreductase subunit VorA; VOR; 2-oxoisovalerate oxidoreductase alpha chain; 2-oxoisovalerate-ferredoxin oxidoreductase subunit alpha; EC 1.-.-.- (characterized)
to candidate WP_048082312.1 EI99_RS12510 ketoisovalerate oxidoreductase

Query= SwissProt::P80907
         (478 letters)



>NCBI__GCF_000746075.1:WP_048082312.1
          Length = 475

 Score =  707 bits (1825), Expect = 0.0
 Identities = 340/474 (71%), Positives = 402/474 (84%)

Query: 1   MTKKVIRKPDSLHEVFERKGGSAPTATHYCAGCGHGILHKLIGEAIDELGIQERSVMISP 60
           M +K+I+KP+S+ + FERKGGSAPTATHYC GCGHGILHKLIGEA+DEL I++R+V+ISP
Sbjct: 1   MEEKIIKKPESILDTFERKGGSAPTATHYCPGCGHGILHKLIGEALDELEIEDRAVLISP 60

Query: 61  VGCAVFAYYYFDCGNVQVAHGRAPAVGTGISRAEDTPVVLLYQGDGDLASIGLNETIQAA 120
           VGCAVFAYYYFDCGNVQVAHGRAPAV TGI+RAED  + +LYQGDGDLASIGLNETIQAA
Sbjct: 61  VGCAVFAYYYFDCGNVQVAHGRAPAVATGITRAEDNAIAMLYQGDGDLASIGLNETIQAA 120

Query: 121 NRGEKMAVFFVNNTVYGMTGGQMAPTTLIGEVTVTCPGGRDPRYAGYPLHMCELLDNLQA 180
           NRGEK+AVFFVNNTVYGMTGGQMAPTTLIGEVTVTCP GRDPR+AGYPLHMCELLDNL A
Sbjct: 121 NRGEKLAVFFVNNTVYGMTGGQMAPTTLIGEVTVTCPTGRDPRFAGYPLHMCELLDNLNA 180

Query: 181 PVFIERVSLADPKSIRKAKRAVKRALEIQRDGKGYAFVEVLSPCPTNLRQDAEGAERFLK 240
           PVFIERVSL+D K IRKAK AVK+AL IQ++ KGYAFVE LSPCPTNLRQDA GAE+F+ 
Sbjct: 181 PVFIERVSLSDVKHIRKAKIAVKKALRIQKENKGYAFVEFLSPCPTNLRQDALGAEKFIN 240

Query: 241 EEMEREFPVKNFRDRSSETEPLIRSESDFSRESLDRIFQIKEDSVPDPVDDPEFREVRVK 300
           EEME+EFP+K FRDR+ E EPL R +SDFS+ESL+++F I  +S    +++P+F E RVK
Sbjct: 241 EEMEKEFPLKRFRDRTKEVEPLCRGKSDFSKESLNKLFNIGSESTGAAINNPDFGEKRVK 300

Query: 301 IAGFGGQGVLSMGLTLAQAACSEGRHTSWYPAYGPEQRGGTSSCGVVISGERVGSPAVDT 360
           IAGFGGQGVLSMGLTLA+A      + S+YPAYGPEQRGG+S+C V++SGE +GSP V+ 
Sbjct: 301 IAGFGGQGVLSMGLTLAEAGMKAQHYVSYYPAYGPEQRGGSSNCAVIMSGEVIGSPVVNE 360

Query: 361 PDVLVAFNQPSLDEFAGDVREGGIVLYDTATADFSKKENLRAIGVPALEIAKEHGTGRAA 420
            DVLVA N+PSL+EF G+VR+GG+++YD++   F   E + AI VPA +IAKEHG  RA 
Sbjct: 361 VDVLVALNKPSLEEFVGEVRDGGLIIYDSSIGYFKAPEGIEAISVPAFKIAKEHGVKRAG 420

Query: 421 NTAMLGVMMALGITGLDEESFRDAIRFTFSGKDKIIDINLKILEAGADWARKNL 474
           NT +LGV+MALG T L EE F+DAI+ TFS K K+I +NL+ILEAGA W R NL
Sbjct: 421 NTVLLGVLMALGYTELPEEVFKDAIKHTFSKKPKLIPVNLEILEAGAKWVRDNL 474


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: 773
Number of extensions: 30
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: 475
Length adjustment: 33
Effective length of query: 445
Effective length of database: 442
Effective search space:   196690
Effective search space used:   196690
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 24 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