GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Dyella japonica UNC79MFTsu3.2

Align 3-ketoacyl-CoA thiolase B, peroxisomal; Acetyl-CoA acyltransferase B; Beta-ketothiolase B; Peroxisomal 3-oxoacyl-CoA thiolase B; EC 2.3.1.155; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate N515DRAFT_2688 N515DRAFT_2688 acetyl-CoA acyltransferase

Query= SwissProt::P07871
         (424 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2688
          Length = 401

 Score =  319 bits (817), Expect = 1e-91
 Identities = 189/400 (47%), Positives = 260/400 (65%), Gaps = 23/400 (5%)

Query: 37  DVVVVHGRRTPIGRAGRGGFKDTTPDELLSAVLTAVL-QDVKLKPECLGDISVGNVL-QP 94
           D  +V   RTP+G+A RG F++T PD++L+ V+ AV+ Q   +    +GD+ VG  + + 
Sbjct: 7   DAYIVAATRTPVGKAPRGVFRNTRPDDMLAHVIRAVMAQAPGIDAHRIGDVIVGCAMPEA 66

Query: 95  GAGAAMARIAQFLSGIPETVPLSAVNRQCSSGLQAVANIAGGIRNGSYDIGMACGVESMT 154
             G  +ARI   L+G+P+TVP   VNR CSSG+QA+A  A  IR G  D+ +A G ESM+
Sbjct: 67  EQGMNVARIGLLLAGLPDTVPGVTVNRFCSSGVQAIAQAADRIRLGEADLMIAAGTESMS 126

Query: 155 LSER-GNPGNISSRLLENEKARDCLIPMGITSENVAERFGISRQKQDAFALASQQKAASA 213
           +    G+   ++  + +NE        MGIT+ENVA+++ ISR++QD FA AS ++A +A
Sbjct: 127 MVPMMGHKVAMNPGIFDNEHI-GIAYGMGITAENVAKQWKISREEQDTFAAASHERALAA 185

Query: 214 QSKGCFRAEIVPVTTTVLDD----------KGDRKTITVSQDEGVRPSTTMEGLAKLKPA 263
              G F+ EI P     LDD          K D + I    DEG RP +T+E L KLKP 
Sbjct: 186 IKAGEFKDEITPFK---LDDHYPDLATRSIKTDSRLIDT--DEGPRPGSTVEVLGKLKPV 240

Query: 264 FKDG---GSTTAGNSSQVSDGAAAVLLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIG 320
           F++G   GS TAGNSSQ SDGA AVLLA  +  +E GL  +    SY+V GV PDIMGIG
Sbjct: 241 FRNGQFGGSVTAGNSSQTSDGAGAVLLASEAAIKEYGLTPIARFVSYSVAGVRPDIMGIG 300

Query: 321 PAYAIPAALQKAGLTVNDIDIFEINEAFASQALYCVEKLGIPAEKVNPLGGAIALGHPLG 380
           P  AIP AL++AG+T + +D  E+NEAFA+Q+L  ++ LG+   K+NPLGGAIALGHPLG
Sbjct: 301 PKEAIPKALKQAGMTQDQLDWIELNEAFAAQSLAVIKDLGLDPSKINPLGGAIALGHPLG 360

Query: 381 CTGARQVVTLLNELKRRGRRAYGVVSMCIGTGMGAAAVFE 420
            TGA +  TL++ ++RR ++ YG+V+MCIGTGMGAA +FE
Sbjct: 361 ATGAIRAATLVHGMRRR-KQKYGMVTMCIGTGMGAAGIFE 399


Lambda     K      H
   0.316    0.133    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: 437
Number of extensions: 20
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 424
Length of database: 401
Length adjustment: 31
Effective length of query: 393
Effective length of database: 370
Effective search space:   145410
Effective search space used:   145410
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 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