GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sphingopyxis indica DS15

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_089217008.1 CHB69_RS16345 acetyl-CoA C-acyltransferase

Query= BRENDA::Q0K368
         (391 letters)



>NCBI__GCF_900188185.1:WP_089217008.1
          Length = 389

 Score =  497 bits (1280), Expect = e-145
 Identities = 248/391 (63%), Positives = 305/391 (78%), Gaps = 2/391 (0%)

Query: 1   MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60
           MA AYIV AVRTAGGR+GG+L+G HP DL A V DA+ +R   D A ++DVI GCVSQ G
Sbjct: 1   MAAAYIVDAVRTAGGRRGGRLAGVHPVDLGAAVYDAIADRNDFDTAAIDDVITGCVSQGG 60

Query: 61  EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120
           EQ  ++ RNA+LAS+LP+S+P  ++DRQCGSSQQA+ FAAQAVMSG  DIV+A+G+ESMT
Sbjct: 61  EQTMDLGRNAVLASKLPDSIPAVTIDRQCGSSQQAMMFAAQAVMSGTQDIVLASGIESMT 120

Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180
           RVPMG  + L  K G G  KSP +E +YPG+ FSQF GAEMI +K+  +++ LDA+AL+S
Sbjct: 121 RVPMGSVATLFMKEGLGNYKSPRLEEKYPGIMFSQFMGAEMIVKKHGFTKDDLDAFALES 180

Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLIAEGGRV 240
           H+RA AAT+ G+F  EI+P+ + T +GA   MH  DEG+R+DATLE I  VKL+ EGG +
Sbjct: 181 HRRARAATEGGKFEREIVPIAIETPEGA--AMHKVDEGIRFDATLEGIAGVKLLQEGGTI 238

Query: 241 TAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVALK 300
           TAAS+SQICDGA+  ++V+E  LK  G+ P AR+H ++V   DPV+MLE PL ATE ALK
Sbjct: 239 TAASSSQICDGASAALIVSEQALKDHGLTPRARIHHISVTAGDPVIMLEEPLFATEKALK 298

Query: 301 KAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTTL 360
           KAG++IGDID +EVNEAFAPVPLAW+K  GAD ARLNVHGGAIALGHPLG SG KLM TL
Sbjct: 299 KAGMKIGDIDAYEVNEAFAPVPLAWMKYLGADHARLNVHGGAIALGHPLGASGTKLMATL 358

Query: 361 VHALHTHGKRYGLQTMCEGGGLANVTIVERL 391
           +  L   G +YGLQTMCEGGG ANVTIVERL
Sbjct: 359 LGVLDATGGKYGLQTMCEGGGQANVTIVERL 389


Lambda     K      H
   0.317    0.132    0.379 

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: 531
Number of extensions: 21
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: 391
Length of database: 389
Length adjustment: 31
Effective length of query: 360
Effective length of database: 358
Effective search space:   128880
Effective search space used:   128880
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 (21.7 bits)
S2: 50 (23.9 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