GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligB in Azospirillum brasilense Sp245

Align protocatechuate 4,5-dioxygenase beta chain (EC 1.13.11.8) (characterized)
to candidate AZOBR_RS26885 AZOBR_RS26885 protocatechuate 3 4-dioxygenase subunit beta

Query= metacyc::MONOMER-15117
         (302 letters)



>FitnessBrowser__azobra:AZOBR_RS26885
          Length = 280

 Score =  281 bits (718), Expect = 2e-80
 Identities = 131/279 (46%), Positives = 190/279 (68%), Gaps = 2/279 (0%)

Query: 1   MARVTTGITSSHIPALGAAIQTGTSDNDYWGPVFKGYQPIRDWIKQPGNMPDVVILVYND 60
           MA++  G+T+SHIPA+G AI     ++ YW P F GY   R+W+ +    PDV I+VYND
Sbjct: 1   MAKIVGGVTTSHIPAIGNAIANELFEDPYWKPFFDGYPKAREWLAEV--KPDVAIVVYND 58

Query: 61  HASAFDMNIIPTFAIGCAETFKPADEGWGPRPVPDVKGHPDLAWHIAQSLILDEFDMTIM 120
           H   F ++ +PTF+IG A  ++  DEGWG +P+P   G P+L+WHI +SL+ DEFD+   
Sbjct: 59  HGLNFFLDKMPTFSIGAAPEYQNKDEGWGLKPLPPYPGDPELSWHIIESLVNDEFDICSC 118

Query: 121 NQMDVDHGCTVPLSMIFGEPEEWPCKVIPFPVNVVTYPPPSGKRCFALGDSIRAAVESFP 180
            +M VDHG TVP+++++ +  + P + IP  VN V +P P+  RC  LG++I  AV S+P
Sbjct: 119 QEMAVDHGFTVPMALLWPDQTQRPVRTIPVAVNTVQHPLPTPARCLKLGEAIGRAVASYP 178

Query: 181 EDLNVHVWGTGGMSHQLQGPRAGLINKEFDLNFIDKLISDPEELSKMPHIQYLRESGSEG 240
           +DL V V GTGG+SHQL G RAG INK+FDL  ++K++ +PE L+K      +R +G++G
Sbjct: 179 KDLKVVVLGTGGLSHQLDGERAGFINKDFDLMCLEKIVDEPEALAKYSIHDLVRLAGAQG 238

Query: 241 VELVMWLIMRGALPEKVRDLYTFYHIPASNTALGAMILQ 279
            EL++WLIMRGAL  KV  +++ YHIP SNT  G ++L+
Sbjct: 239 AELILWLIMRGALGRKVSKVHSNYHIPISNTGAGLLVLE 277


Lambda     K      H
   0.319    0.138    0.439 

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: 323
Number of extensions: 13
Number of successful extensions: 2
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: 302
Length of database: 280
Length adjustment: 26
Effective length of query: 276
Effective length of database: 254
Effective search space:    70104
Effective search space used:    70104
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: 48 (23.1 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