Alignments for a candidate for lutB in Dechlorosoma suillum PS

GapMind for catabolism of small carbon sources

Alignments for a candidate for lutB in Dechlorosoma suillum PS

Align Lactate utilization protein B (characterized)
to candidate Dsui_0126 Dsui_0126 (4Fe-4S) cluster-containing protein

Query= SwissProt::O07021
         (479 letters)



>FitnessBrowser__PS:Dsui_0126
          Length = 479

 Score =  377 bits (968), Expect = e-109
 Identities = 196/481 (40%), Positives = 298/481 (61%), Gaps = 12/481 (2%)

Query: 3   MKIGTDAFKERVSQGIDNEFMRGAVSGAQERLRTRRLEAAEEL------GNWEEWRSLSE 56
           M++ +  F+ R ++ + +  ++  + GA++     R     E       G++E  R +  
Sbjct: 1   MEVKSLQFRARAAERLADPALQSKLGGAKQLFVGGRARVVAEFDSVGQAGDFETLRGIGA 60

Query: 57  EIRQHVLENLDFYLGQLAENVAKRGGHVYFAKTAEEASSYIRDVIQKKNGKKIVKSKSMV 116
           EIR   L +LD +L          G  V +A+   EA   I D+ ++   KK++KSKSM+
Sbjct: 61  EIRDTALTDLDAWLEAFEAKATATGATVLWARDGREAQQLIVDIAKRHGVKKVIKSKSML 120

Query: 117 TEEINLNEVLEKEGCEVVETDLGEYILQIDDHDPPSHIVAPALHKNKEQIRDVFKERLDY 176
           +EE  LNE LE  G + VETDLGEYILQ+   +PPSHI+APA+HKNKE++ ++F      
Sbjct: 121 SEEAGLNEGLEAAGVQSVETDLGEYILQLAK-EPPSHILAPAIHKNKEEVDELFARCHGR 179

Query: 177 QHTEKPE----ELVMHARAILRKKFLEADIGITGCNFAIADTGSVSLVTNEGNGRLVSTL 232
             T + +     L   AR  LR+ FL AD+GITG NF +A+TGSV+LVTNEGNGR+V+TL
Sbjct: 180 PVTPEGQIDIPALTREARVALREHFLSADMGITGGNFLVAETGSVALVTNEGNGRMVTTL 239

Query: 233 PKTQITVMGMERIVPSFSEFEVLVSMLTRSAVGQRLTSYITALTGPKLEGEVDGPEEFHL 292
           P+  + V+G+E+++P+  +   L+ +LTRSA GQ +++Y++ LTGP+ EG V+GPE  + 
Sbjct: 240 PRVHVAVVGIEKVIPTLEDLSALLRLLTRSATGQTISNYVSLLTGPRAEGAVEGPEHMYF 299

Query: 293 VIVDNGRSNILGTEFQSVLQCIRCAACINVCPVYRHVGGHSYGSIYSGPIGAVLSPLLGG 352
           V++DNGR+ ++G +FQ +L+CIRC AC+N CPVY+ +GGH+YG +Y GP+G+VL+PL  G
Sbjct: 300 VLMDNGRAGLVGGDFQEMLRCIRCGACMNHCPVYQSIGGHAYGWVYPGPMGSVLTPLYTG 359

Query: 353 YDDYKELPYASSLCAACSEACPVKIPLHELLLKHRQNIVEKEGRAPISEKLAMKAFGLGA 412
            +   +LP A++LC  CS  CPVKIPL ELL K R+  +E E R P  E+ A++ +G  A
Sbjct: 360 LEQAPDLPQAATLCGQCSIVCPVKIPLPELLRKLREKQMETELR-PWQERWALRTWGFFA 418

Query: 413 SSLSLYKMGSKWAPAAMTPFTEDEKISKGPGPLKNWTQIRDFPAPHKSRFRDWFADRETS 472
           +   LY + +     A+      +   +    +  W++ RDFPAP    FR+ +A R   
Sbjct: 419 ARPRLYALAAGLGARALKLLAGGKASIRTLPGVPEWSRGRDFPAPQGKTFRELYAARRRQ 478

Query: 473 E 473
           +
Sbjct: 479 D 479


Lambda     K      H
   0.316    0.134    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: 495
Number of extensions: 14
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: 479
Length of database: 479
Length adjustment: 34
Effective length of query: 445
Effective length of database: 445
Effective search space:   198025
Effective search space used:   198025
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: 51 (24.3 bits)

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

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Protein sequences (fasta format)
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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 paper from 2022 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