GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3033 in Dechlorosoma suillum PS

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate Dsui_0126 Dsui_0126 (4Fe-4S) cluster-containing protein

Query= uniprot:Q726S3
         (717 letters)



>FitnessBrowser__PS:Dsui_0126
          Length = 479

 Score =  303 bits (777), Expect = 1e-86
 Identities = 181/468 (38%), Positives = 262/468 (55%), Gaps = 20/468 (4%)

Query: 9   EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEV-------ADAKDHA 61
           ++R    E L +  L++ +      +   RA    + D      +        A+ +D A
Sbjct: 7   QFRARAAERLADPALQSKLGGAKQLFVGGRARVVAEFDSVGQAGDFETLRGIGAEIRDTA 66

Query: 62  AKNMDTLYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHL 121
             ++D     F+A+A   G  V  AR   EA ++I  IA+ +  KK IKSKSM +EE  L
Sbjct: 67  LTDLDAWLEAFEAKATATGATVLWARDGREAQQLIVDIAKRHGVKKVIKSKSMLSEEAGL 126

Query: 122 NHRLEEDNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSE-----VTKQKQ 176
           N  LE   V+ +ETDLGE+I+Q+  E PSH++ PAIH ++ +V +LF+      VT + Q
Sbjct: 127 NEGLEAAGVQSVETDLGEYILQLAKEPPSHILAPAIHKNKEEVDELFARCHGRPVTPEGQ 186

Query: 177 EVDIQRLVKVARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVA 236
            +DI  L + AR  LR HF +ADMGI+G NF VAETG++ LVTNEGN R+VTTLPRVHVA
Sbjct: 187 -IDIPALTREARVALREHFLSADMGITGGNFLVAETGSVALVTNEGNGRMVTTLPRVHVA 245

Query: 237 LAGLDKLVPTLHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDN 296
           + G++K++PTL D    L++L R+ATGQ I++YV+ + G    E  V+G + M+ V +DN
Sbjct: 246 VVGIEKVIPTLEDLSALLRLLTRSATGQTISNYVSLLTGP-RAEGAVEGPEHMYFVLMDN 304

Query: 297 GRRALAEDPLFSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKA 356
           GR  L     F ++LRC+RCGAC N CPVY+ +GGH  G +Y G +G +LT  + G ++A
Sbjct: 305 GRAGLVGGD-FQEMLRCIRCGACMNHCPVYQSIGGHAYGWVYPGPMGSVLTPLYTGLEQA 363

Query: 357 RNLVQNCINCESCKHICAGGIDLPRLIKEIRARLNEEEGMPVE----TTLMGKMLKNRKL 412
            +L Q    C  C  +C   I LP L++++R +  E E  P +        G      +L
Sbjct: 364 PDLPQAATLCGQCSIVCPVKIPLPELLRKLREKQMETELRPWQERWALRTWGFFAARPRL 423

Query: 413 FHTLLRFAKWAQKPVTGGTPYIRHLPQIFAKDHGFKALPAIADKPFRD 460
           +         A K + GG   IR LP +     G +  PA   K FR+
Sbjct: 424 YALAAGLGARALKLLAGGKASIRTLPGVPEWSRG-RDFPAPQGKTFRE 470


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: 791
Number of extensions: 38
Number of successful extensions: 5
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: 479
Length adjustment: 37
Effective length of query: 680
Effective length of database: 442
Effective search space:   300560
Effective search space used:   300560
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