GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3033 in Desulfovibrio vulgaris Miyazaki F

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 8501127 DvMF_1863 protein of unknown function DUF224 cysteine-rich region domain protein (RefSeq)

Query= uniprot:Q726S3
         (717 letters)



>FitnessBrowser__Miya:8501127
          Length = 430

 Score =  206 bits (525), Expect = 1e-57
 Identities = 130/421 (30%), Positives = 210/421 (49%), Gaps = 13/421 (3%)

Query: 306 LFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTY---FFHGRDKARNLVQN 362
           L  Q++ C++CG C  VCPV+      K   +  G I L+        H     +  +  
Sbjct: 14  LDDQMVGCMKCGMCQAVCPVFAET--MKEADVTRGKIALLENLAKEMIHDAAGVQEKLNK 71

Query: 363 CINCESCKHICAGGIDLPRLIKEIRARLNEEEGM-PVETTLMGKMLKNRKLFHTLLRFAK 421
           C+ C SC   C  G+ +  +    R  +N   G+ PV+  ++  ML    LF+ LL    
Sbjct: 72  CLLCGSCGANCPSGVKVMDIFLRARVIVNTYMGLSPVKKAILRGMLTKPALFNALLDLGS 131

Query: 422 WAQKPVTGGTPYI--RHLPQIFAKDHGFKALPAIADKPFRDEWETVRPRIAKPKLRIALF 479
             Q   T     +      ++ +   G +    +A +    + + +     K   R+A F
Sbjct: 132 KFQGIFTSKVDDLLGSSCSKVLSPVIGDRHFVGLAKQSLHSKIKALDTPAGKSGKRVAFF 191

Query: 480 SGCVQDFVYPEQMKAAVKVIASQNVDIDFPMDQSCCGLPVQMMGEREATIEVARQNVMAF 539
            GC+ D ++    +A +KV     V +  P  Q+CCG+P    G+R A  ++ + N+  F
Sbjct: 192 PGCLGDKMFVSVAEACLKVFEHHGVGVYMPEGQACCGIPAISSGDRVAYDKLVKINLDLF 251

Query: 540 DAARYDYIVTLCASCASHLKETYPKLLTGHP-EMTTRVRQFSNKIIDFSSFVHDVLGMKS 598
               +DY+VT CA+C + +KE +PKL+  +P  M  ++R   +K++D + FV DVLG+K 
Sbjct: 252 SKGGFDYLVTPCATCTATIKEIWPKLMDEYPATMRDQIRALHDKVMDVNQFVVDVLGVKP 311

Query: 599 DA-FKGGSNEKVAYHSSCHLCRGLGVVEQPRNLIAASGA-TYCKAEEEDVCCGFGGTFSA 656
           +A  KGG   KV +H SCH+ + LGV  QPR LI  +      +  E D CCG GG+F+ 
Sbjct: 312 EAPAKGG--VKVTFHDSCHMKKSLGVTSQPRALIGMNPKYELVEMAECDRCCGSGGSFNL 369

Query: 657 KFPELSAELLRKKLDNVEATGAGRLVADCPGCIMQLRGGMEKRGGKVKVGHVAELLAENL 716
              +LS ++  +K DN+ ATGA  +   CP C++Q+   + + G KV V H  EL A++L
Sbjct: 370 YHYDLSKQIGERKRDNILATGAQIVSTGCPACMLQMTDMLSQHGAKVAVKHSIELYADSL 429

Query: 717 K 717
           +
Sbjct: 430 R 430


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: 729
Number of extensions: 47
Number of successful extensions: 7
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: 430
Length adjustment: 36
Effective length of query: 681
Effective length of database: 394
Effective search space:   268314
Effective search space used:   268314
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: 53 (25.0 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