Aligments for a candidate for DVU3033 in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Aligments for a candidate for DVU3033 in Desulfovibrio vulgaris Miyazaki F

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 8501132 DvMF_1868 protein of unknown function DUF162 (RefSeq)

Query= uniprot:Q726S3
         (717 letters)



>lcl|FitnessBrowser__Miya:8501132 DvMF_1868 protein of unknown
           function DUF162 (RefSeq)
          Length = 716

 Score = 1236 bits (3199), Expect = 0.0
 Identities = 602/717 (83%), Positives = 665/717 (92%), Gaps = 1/717 (0%)

Query: 1   MQNSKTLKEYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADAKDH 60
           MQ +KTLKEYRKEL+ESLDNEFLR AMDKFA AY  SRANAF+ +DEKA+IAEVADAKD 
Sbjct: 1   MQTAKTLKEYRKELRESLDNEFLREAMDKFATAYPVSRANAFRGLDEKAMIAEVADAKDA 60

Query: 61  AAKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETH 120
           AAKNMD LYAQFKAEA+KRGVKVH+A+ AAEANEIIARIA+++NCKK +KSKSMTAEET 
Sbjct: 61  AAKNMDALYAQFKAEAKKRGVKVHMAKDAAEANEIIARIAKNSNCKKIVKSKSMTAEETL 120

Query: 121 LNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSEVTKQKQEVDI 180
           LNHRLEED +EVIETDLGEWIIQ+RHEGP+HMVMPAIHLSRYQVADLFSEVTKQKQEVDI
Sbjct: 121 LNHRLEEDGLEVIETDLGEWIIQLRHEGPTHMVMPAIHLSRYQVADLFSEVTKQKQEVDI 180

Query: 181 QRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGL 240
           QRLVKVARRELR HFATADMGISGANFA+AE+GTIGLVTNEGNARLVTTLPRVHVAL GL
Sbjct: 181 QRLVKVARRELRQHFATADMGISGANFAIAESGTIGLVTNEGNARLVTTLPRVHVALCGL 240

Query: 241 DKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRA 300
           DKL P+L+DAL+SL+VLPRNATGQAITSYVTWI GANEC+A  D +KEMHIVFLDNGRRA
Sbjct: 241 DKLTPSLNDALKSLRVLPRNATGQAITSYVTWITGANECKAAADEKKEMHIVFLDNGRRA 300

Query: 301 LAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLV 360
           LA+DPLFSQV+RCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHG+DKARNLV
Sbjct: 301 LAQDPLFSQVMRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGKDKARNLV 360

Query: 361 QNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRFA 420
           QNCINCESCK ICAGGIDLPRLIKEIRARL+EE+G PVE TL+GK+LKNRKLFHTLLRF 
Sbjct: 361 QNCINCESCKSICAGGIDLPRLIKEIRARLSEEDGAPVEATLLGKVLKNRKLFHTLLRFG 420

Query: 421 KWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPKLRIALFS 480
           K+AQKPVTGGTPY+RHLPQ+F KDHGF+ALPAIADK FRDEWET+RPR++  KLR+ALFS
Sbjct: 421 KFAQKPVTGGTPYLRHLPQMFMKDHGFRALPAIADKAFRDEWETIRPRVSNAKLRVALFS 480

Query: 481 GCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVARQNVMAFD 540
           GCVQDFVYPEQMKAAVKV+AS+ V++DFPMDQSCCGLPVQMM ER+ATI+VARQNVMAFD
Sbjct: 481 GCVQDFVYPEQMKAAVKVLASRGVEMDFPMDQSCCGLPVQMMAERQATIDVARQNVMAFD 540

Query: 541 AARYDYIVTLCASCASHLKETYPKLLTGHPEMTTRVRQFSNKIIDFSSFVHDVLGMKSDA 600
           AA+YDYI+TLCASCASHLKE YP +L G  +MT +V+ F++K+IDFSSFVHDVLGM +D 
Sbjct: 541 AAKYDYILTLCASCASHLKEGYPNILAGQTDMTGKVKLFASKVIDFSSFVHDVLGMTADD 600

Query: 601 FKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAASGATYCKAEEEDVCCGFGGTFSAKFPE 660
           FK G  EKVAYHSSCHLCRGLGVVEQPR LIA+SG+ YC A+EE VCCGFGGTFS KFPE
Sbjct: 601 FK-GKGEKVAYHSSCHLCRGLGVVEQPRALIASSGSEYCPAQEEAVCCGFGGTFSMKFPE 659

Query: 661 LSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAELLAENLK 717
           LS ELL KKL+N EATGA R+VADCPGCIMQ+RGG EKRG ++KVGH+AELLAENLK
Sbjct: 660 LSKELLDKKLNNAEATGATRMVADCPGCIMQIRGGAEKRGSRMKVGHIAELLAENLK 716


Lambda     K      H
   0.321    0.135    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: 1609
Number of extensions: 63
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: 717
Length of database: 716
Length adjustment: 40
Effective length of query: 677
Effective length of database: 676
Effective search space:   457652
Effective search space used:   457652
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 (21.9 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources