GapMind for catabolism of small carbon sources

 

Alignments for a candidate for andAc in Azospirillum thiophilum BV-S

Align Anthranilate 1,2-dioxygenase large subunit; EC 1.14.12.1 (characterized)
to candidate WP_045585170.1 AL072_RS30310 Rieske 2Fe-2S domain-containing protein

Query= SwissProt::Q84BZ3
         (423 letters)



>NCBI__GCF_001305595.1:WP_045585170.1
          Length = 429

 Score =  144 bits (363), Expect = 5e-39
 Identities = 76/205 (37%), Positives = 113/205 (55%), Gaps = 12/205 (5%)

Query: 28  RVPYKVFSSRAVYDREQERIFRGPTWNFVALEAEIPNAGDFKSTFVGDTPVVVTRTEDGA 87
           R    +++  A++++E +RIF    W +VA  +E+  AGD+KST+VG  PVVV R     
Sbjct: 27  RAHTSLYTDPAIFEQEMDRIFAN-CWVWVAHVSEVKEAGDYKSTYVGRQPVVVVRDRKQK 85

Query: 88  LSAWVNRCAHRGAQVCRKSRGNASSHTCVYHQWSFDNEGNLLGVPFRRGQKGMTGMPADF 147
           +   +NRC HR A VC + +G  +S  C YH WS+  +G+L GVP               
Sbjct: 86  IHVLLNRCRHRAATVCEEKKGKTNSFVCPYHGWSYGLDGSLRGVPHPESYGQC------L 139

Query: 148 DPKQHGLRKLRVDSYRGLVFATFSDDVAPLPDYLGAQMRPWIDRIFHK----PIEYLGCT 203
           D  ++ L+ LRV+ Y G+VFATF +D+ PL D+LG   + W+D    +    PI+  G  
Sbjct: 140 DKGEYPLKSLRVEEYAGMVFATFREDIEPLADWLG-PAKKWMDLFMRQGGGYPIKVAGEH 198

Query: 204 RQYSKSNWKLYMENVKDPYHASMLH 228
           R     NWK+ +EN  D YH  ++H
Sbjct: 199 RFRFPGNWKIQLENTTDGYHFPVVH 223


Lambda     K      H
   0.321    0.136    0.420 

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: 482
Number of extensions: 25
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 423
Length of database: 429
Length adjustment: 32
Effective length of query: 391
Effective length of database: 397
Effective search space:   155227
Effective search space used:   155227
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 (21.8 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 24 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