GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Geobacter daltonii FRC-32

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_012645203.1 GEOB_RS00490 acetyl-CoA C-acyltransferase

Query= SwissProt::P14611
         (393 letters)



>NCBI__GCF_000022265.1:WP_012645203.1
          Length = 399

 Score =  360 bits (924), Expect = e-104
 Identities = 192/399 (48%), Positives = 265/399 (66%), Gaps = 8/399 (2%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M + VIV A RT VGK+GG+L  + + +L A  I   ++R  + P  + +V++G    AG
Sbjct: 1   MREAVIVDAVRTPVGKWGGALKNVRSDDLAAHCIAELVKRTKIDPNLIEDVVLGCTNQAG 60

Query: 61  S-GQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMS 119
              +N  R AA+ AGLP      TIN++C SGL A+  AA AI  G+ ++ +AGG E+M+
Sbjct: 61  EDNRNVGRMAALLAGLPYSAAGQTINRLCASGLNAINSAAQAIKVGEGDVFIAGGTESMT 120

Query: 120 AAPHVLPGSRDGFRMGDAKLVDTMIV-----DGLWDVYNQYHMGITAENVAKEYGITREA 174
            AP V+  S   F   D K+ DT+I        + + Y +  MG TAENVA  YG+TR+ 
Sbjct: 121 RAPFVMAKSESPFSR-DVKVFDTVIGWRFTNPKMTEPYAKEGMGETAENVAVRYGLTRQE 179

Query: 175 QDEFAVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVR-QGATLDSMSGLK 233
           QDEFA+ +Q K  AA  AGKF++EIVPV+IPQ+KGDP+    DEF R    T++ ++ L 
Sbjct: 180 QDEFALDTQKKWAAADAAGKFNDEIVPVVIPQKKGDPIIVSRDEFPRGNDVTMEQLAKLP 239

Query: 234 PAFDKAGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGP 293
            AF K GTVTA N+SG+NDGAAA+++M A  AK+LG  PLA + + A AG DP  MG+GP
Sbjct: 240 AAFRKDGTVTAGNSSGINDGAAALLLMEAETAKKLGYKPLARVVASAVAGCDPSYMGLGP 299

Query: 294 VPASKRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGA 353
           +PA ++ L RA    +D+DL E+NEAFAAQ++   +++G D +KVNVNGG+IAIGHP+G+
Sbjct: 300 IPAIQKVLKRANLKIEDIDLFELNEAFAAQSIPCIRELGIDPAKVNVNGGSIAIGHPLGS 359

Query: 354 SGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           +G RI  TL+HEMKRR+A+ G+ SLCIG G G+A   ER
Sbjct: 360 TGARITATLVHEMKRRNARYGIVSLCIGVGQGIATVFER 398


Lambda     K      H
   0.315    0.131    0.369 

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: 392
Number of extensions: 12
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: 393
Length of database: 399
Length adjustment: 31
Effective length of query: 362
Effective length of database: 368
Effective search space:   133216
Effective search space used:   133216
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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