GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Caulobacter crescentus NA1000

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate CCNA_00820 CCNA_00820 3-ketoacyl-CoA thiolase

Query= BRENDA::Q0K368
         (391 letters)



>FitnessBrowser__Caulo:CCNA_00820
          Length = 390

 Score =  612 bits (1578), Expect = e-180
 Identities = 302/391 (77%), Positives = 348/391 (89%), Gaps = 1/391 (0%)

Query: 1   MAEAYIVAAVRTAGGRKGGKLSGWHPADLAAQVLDALVERTGADPALVEDVIMGCVSQVG 60
           M EAYIVAA RTAGGRKGG++SGWHPADLA +VL+ALV+R+GADPAL+EDVIMGCV QVG
Sbjct: 1   MGEAYIVAAARTAGGRKGGRVSGWHPADLAGEVLNALVDRSGADPALIEDVIMGCVGQVG 60

Query: 61  EQAGNVARNAILASRLPESVPGTSVDRQCGSSQQALHFAAQAVMSGAMDIVIAAGVESMT 120
           EQA N+ARNA+LAS+LPESVP TSVDRQCGSSQQ++HFAA  VMSGAMDIVIAAGVESM+
Sbjct: 61  EQAINIARNAVLASKLPESVPATSVDRQCGSSQQSIHFAAATVMSGAMDIVIAAGVESMS 120

Query: 121 RVPMGLSSQLPAKNGFGVPKSPGIEARYPGVQFSQFTGAEMIARKYDLSREQLDAYALQS 180
           RVPMGLSS LP KNGFG  KSP +E RYPG+QFSQF GAEM+A+KYDLSREQLDA+AL S
Sbjct: 121 RVPMGLSSALPYKNGFGTYKSPRMEERYPGIQFSQFAGAEMLAKKYDLSREQLDAFALAS 180

Query: 181 HQRAIAATKSGRFTAEILPVEVRTADGANGEMHTTDEGVRYDATLESIGSVKLIAEGGRV 240
           HQRA+AATK G+F AEI+P++V   DG + E H  DEG+R+DAT+ESIG VKL++E GR+
Sbjct: 181 HQRAMAATKGGKFAAEIVPIKVTLPDG-SVETHDADEGIRWDATMESIGGVKLLSEDGRL 239

Query: 241 TAASASQICDGAAGLMVVNEAGLKKLGVKPLARVHAMTVIGHDPVVMLEAPLPATEVALK 300
           TAA++SQICDGAAG+M+VNE GLK LGV PLAR+H MTVIGHDPV+MLEAP+PAT+ AL+
Sbjct: 240 TAATSSQICDGAAGVMIVNERGLKALGVAPLARIHHMTVIGHDPVIMLEAPIPATQKALE 299

Query: 301 KAGLRIGDIDLFEVNEAFAPVPLAWLKATGADPARLNVHGGAIALGHPLGGSGAKLMTTL 360
           +AG++I DIDL+EVNEAFA VP AWL+ TG DP +LNV+GGAIALGHPLGGSGAKLMTTL
Sbjct: 300 RAGMKIDDIDLYEVNEAFASVPTAWLQVTGGDPDKLNVNGGAIALGHPLGGSGAKLMTTL 359

Query: 361 VHALHTHGKRYGLQTMCEGGGLANVTIVERL 391
           VHAL   G RYGLQTMCEGGGLANVTIVERL
Sbjct: 360 VHALKDRGARYGLQTMCEGGGLANVTIVERL 390


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: 605
Number of extensions: 22
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: 390
Length adjustment: 31
Effective length of query: 360
Effective length of database: 359
Effective search space:   129240
Effective search space used:   129240
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 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