GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Azospirillum brasilense Sp245

Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate AZOBR_RS14115 AZOBR_RS14115 (3S)-malyl-CoA thiolesterase

Query= BRENDA::Q8N0X4
         (340 letters)



>FitnessBrowser__azobra:AZOBR_RS14115
          Length = 291

 Score =  136 bits (343), Expect = 6e-37
 Identities = 89/294 (30%), Positives = 148/294 (50%), Gaps = 14/294 (4%)

Query: 44  PRRAVLYVPGNDEKKIKKIPSLNVDCAVLDCEDGVAANKKNEARLRIVKTLEDIDLGPTE 103
           PRR+VLY+PG++ + ++K  SL  D  +LD ED VA + K EAR  I  ++     G  E
Sbjct: 7   PRRSVLYMPGSNTRALEKGRSLPADGLILDLEDAVAPDAKAEARATIKASIAAGGYGGRE 66

Query: 104 KCVRVNSVSSGLAEEDLETLLQSRVLPSSLMLPKVESPEEIQWFADKFSFHLKGRKLEQP 163
             VR N +++    +DL     S     +++LPKVESP+ ++    +    L+       
Sbjct: 67  LVVRTNGLNTPWGYDDLVMAASSGA--DAVLLPKVESPDMVR----QAEAVLRANGSPDG 120

Query: 164 MNLIPFVETAMGLLNFKAVCEETLKVGPQVGLFLDAVVFGGEDFRASIGATSSKETLDIL 223
             +   +ET +G+LN K +   + K+G         +V G  D    + A  +++ L +L
Sbjct: 121 QTIWCMMETPLGMLNTKEIAGASPKLG--------GLVMGTSDLAKDLHAAHTRDRLPML 172

Query: 224 YARQKIVVIAKAFGLQAIDLVYIDFRDGAGLLRQSREGAAMGFTGKQVIHPNQIAVVQEQ 283
            +    ++ A+A+GL  +D V++D  D AG      +G  +GF GK +IHP  IA     
Sbjct: 173 TSLGLCLLAARAYGLAILDGVHLDLNDDAGFGESCVQGRELGFDGKTLIHPKTIAACNAA 232

Query: 284 FSPSPEKIKWAEELIAAFKEHQQLGKGAFTFQGSMIDMPLLKQAQNTVTLATSI 337
           F+PS E++  A  +I A  E    GKG     G +++   ++ A+  V +A +I
Sbjct: 233 FAPSEEEVAQAHRIIQAHAEAVAQGKGVVLVDGRLVENLHVENARRLVAMAEAI 286


Lambda     K      H
   0.319    0.135    0.378 

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: 188
Number of extensions: 9
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: 340
Length of database: 291
Length adjustment: 27
Effective length of query: 313
Effective length of database: 264
Effective search space:    82632
Effective search space used:    82632
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