GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3033 in Cupriavidus basilensis 4G11

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate RR42_RS21285 RR42_RS21285 (Fe-S)-binding protein

Query= uniprot:Q726S3
         (717 letters)



>FitnessBrowser__Cup4G11:RR42_RS21285
          Length = 476

 Score =  290 bits (741), Expect = 1e-82
 Identities = 161/413 (38%), Positives = 232/413 (56%), Gaps = 3/413 (0%)

Query: 9   EYRKELQESLDNEFLRNAMDKFAVAYRASRANAFKDIDEKAIIAEVADA-KDHAAKNMDT 67
           +++   + +LD+  LR++        +A RA  F D DE   + ++ +A + HA   +  
Sbjct: 8   DFKARSRAALDDPKLRSSFRGAMDFLQAKRAVQFPDGDELEQLRDLGEAIRQHALSQLPD 67

Query: 68  LYAQFKAEAEKRGVKVHLARTAAEANEIIARIARDNNCKKAIKSKSMTAEETHLNHRLEE 127
           L  Q + +    GV+VH A TA EAN I+  IA+     + IK KSM +EE  LNH L E
Sbjct: 68  LLVQLEDKLTAAGVQVHWAETADEANAIVHGIAQARQASRVIKGKSMASEEIELNHYLAE 127

Query: 128 DNVEVIETDLGEWIIQMRHEGPSHMVMPAIHLSRYQVADLFSE-VTKQKQEVDIQRLVKV 186
             ++ IE+D+GE+I+Q+  E PSH+VMPAIH +R  +A+LF + +       D+  L++ 
Sbjct: 128 RGIDCIESDMGEYIVQLAGEKPSHIVMPAIHKTRGDIAELFEQHIPGTPYTEDVDELIQT 187

Query: 187 ARRELRTHFATADMGISGANFAVAETGTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPT 246
            RR LR  F  AD+G+SG NFA A+TGT+ LV NEGN RL TT+P VH+A+ G++K+V  
Sbjct: 188 GRRALRQEFVNADIGLSGVNFAAADTGTLWLVENEGNGRLSTTVPDVHIAIMGMEKVVAR 247

Query: 247 LHDALRSLKVLPRNATGQAITSYVTWIGGANECEACVDGRKEMHIVFLDNGRRALAEDPL 306
           L   +    +L R+ATGQAIT+Y   I G        DG +E+H+V LDNGR     D  
Sbjct: 248 LEHIVPLASLLTRSATGQAITTYFNLISGPRRAGE-RDGPREVHLVLLDNGRSQAYADEQ 306

Query: 307 FSQVLRCVRCGACANVCPVYRLVGGHKMGHIYIGAIGLILTYFFHGRDKARNLVQNCINC 366
               L+C+RCGAC N CPVY  +GGH  G  Y G IG I++    G D   +L      C
Sbjct: 307 LRATLQCIRCGACMNHCPVYTRIGGHAYGTTYPGPIGKIISPHLLGLDATADLATASSLC 366

Query: 367 ESCKHICAGGIDLPRLIKEIRARLNEEEGMPVETTLMGKMLKNRKLFHTLLRF 419
            +C  +C   I +P+L+  +R   N +    V   L G+  K  +  H + RF
Sbjct: 367 GACGEVCPVRIPIPQLLIRLRTEANRDPSEQVAHPLRGQGTKFSRGEHLVWRF 419


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: 719
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: 476
Length adjustment: 36
Effective length of query: 681
Effective length of database: 440
Effective search space:   299640
Effective search space used:   299640
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