GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lutB 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:E4PLR6
         (483 letters)



>FitnessBrowser__Miya:8501132
          Length = 716

 Score =  284 bits (726), Expect = 8e-81
 Identities = 153/371 (41%), Positives = 222/371 (59%), Gaps = 7/371 (1%)

Query: 27  LRNNF-RVAMDSLMT----KRANAFPDADEREGLRELGNRIKAGALSRLPDLLEQLEQKL 81
           L N F R AMD   T     RANAF   DE+  + E+ +  K  A   +  L  Q + + 
Sbjct: 18  LDNEFLREAMDKFATAYPVSRANAFRGLDEKAMIAEVADA-KDAAAKNMDALYAQFKAEA 76

Query: 82  TENGVKVHWAETVEEANSLVHGIIEARKGSQVVKGKSMVSEEMEMNDYLAERGVECLESD 141
            + GVKVH A+   EAN ++  I +     ++VK KSM +EE  +N  L E G+E +E+D
Sbjct: 77  KKRGVKVHMAKDAAEANEIIARIAKNSNCKKIVKSKSMTAEETLLNHRLEEDGLEVIETD 136

Query: 142 MGEYIVQLDNEKPSHIIMPAIHKNARQVSKLFHDKLGEPETEDVNQLIQIGRRTLRRKFM 201
           +GE+I+QL +E P+H++MPAIH +  QV+ LF +   + +  D+ +L+++ RR LR+ F 
Sbjct: 137 LGEWIIQLRHEGPTHMVMPAIHLSRYQVADLFSEVTKQKQEVDIQRLVKVARRELRQHFA 196

Query: 202 EADVGVSGVNFAIAETGTLLLVENEGNGRMSTTAPPVHIAVTGIEKVVPNLRDVVPLVSL 261
            AD+G+SG NFAIAE+GT+ LV NEGN R+ TT P VH+A+ G++K+ P+L D +  + +
Sbjct: 197 TADMGISGANFAIAESGTIGLVTNEGNARLVTTLPRVHVALCGLDKLTPSLNDALKSLRV 256

Query: 262 LTRSALGQPITTYVNLISGPRK-PDELDGPEEVHLVLLDNGRTGAFADAQMRQTLNCIRC 320
           L R+A GQ IT+YV  I+G  +     D  +E+H+V LDNGR     D    Q + C+RC
Sbjct: 257 LPRNATGQAITSYVTWITGANECKAAADEKKEMHIVFLDNGRRALAQDPLFSQVMRCVRC 316

Query: 321 GACMNHCPVYTRVGGHTYGEVYPGPIGKIITPHMAGLDKVPDHPSASSLCGACGEVCPVK 380
           GAC N CPVY  VGGH  G +Y G IG I+T    G DK  +       C +C  +C   
Sbjct: 317 GACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGKDKARNLVQNCINCESCKSICAGG 376

Query: 381 IPIPELLQRLR 391
           I +P L++ +R
Sbjct: 377 IDLPRLIKEIR 387


Lambda     K      H
   0.317    0.135    0.403 

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: 762
Number of extensions: 28
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 483
Length of database: 716
Length adjustment: 37
Effective length of query: 446
Effective length of database: 679
Effective search space:   302834
Effective search space used:   302834
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 (21.6 bits)
S2: 53 (25.0 bits)

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

Links

Downloads

Related tools

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