GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Halioglobus japonicus S1-36

Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_084198673.1 C0029_RS06075 acetyl-CoA C-acyltransferase family protein

Query= SwissProt::Q0KBP1
         (394 letters)



>NCBI__GCF_002869505.1:WP_084198673.1
          Length = 395

 Score =  501 bits (1290), Expect = e-146
 Identities = 251/391 (64%), Positives = 305/391 (78%), Gaps = 1/391 (0%)

Query: 3   REVVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEP 62
           REVVV+SGVR+AI  FGGSLKDVAP E+   VV EA+ R+ +   D+GHVV GNV  ++ 
Sbjct: 4   REVVVLSGVRSAIADFGGSLKDVAPTEVAGQVVAEAVKRSGLEPTDIGHVVIGNVTHSDR 63

Query: 63  RDMYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSR 122
           RDMY+ R AA+ GG+ I  PALTVNRLCGSGLQ+++SAAQ ILLGD D A+ GGAESMSR
Sbjct: 64  RDMYMSRTAALKGGLPIETPALTVNRLCGSGLQSVISAAQMILLGDCDAAVAGGAESMSR 123

Query: 123 APYLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALE 182
            PY  P AR+GARMGD  +VD M+GAL  P    HMG+TAEN+A +Y +SR +QDE A E
Sbjct: 124 VPYWLPNARFGARMGDGQMVDAMMGALTCPMGDTHMGITAENLADKYSVSREEQDELAAE 183

Query: 183 SHRRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGT 242
           SHRRA  A + G F+ QI+P+  K RKG V FD DEHVR+DA  +DM KLRP F K++G+
Sbjct: 184 SHRRAQQAQEEGRFESQILPIEIKTRKGTVVFDKDEHVRNDAKAEDMAKLRPAF-KKDGS 242

Query: 243 VTAGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIAL 302
           VTAGNASGLND AAAVV+MER+EAE +GLKP+A++V Y  A VDP  MGIGP PA +  +
Sbjct: 243 VTAGNASGLNDGAAAVVLMERSEAEAKGLKPMAKMVGYAVAAVDPAIMGIGPAPAVRQLM 302

Query: 303 ERAGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVK 362
           E+ G+ + D+D+ E NEAFAAQA +V K L LDPAKVNPNGSGISLGHPIGATG+++TVK
Sbjct: 303 EKTGVAIEDVDIWECNEAFAAQALSVVKELDLDPAKVNPNGSGISLGHPIGATGSMLTVK 362

Query: 363 ALHELNRVQGRYALVTMCIGGGQGIAAIFER 393
           A++EL R   RYA+VTMCIGGGQGIAA+FER
Sbjct: 363 AVYELERTGARYAVVTMCIGGGQGIAALFER 393


Lambda     K      H
   0.318    0.134    0.381 

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: 485
Number of extensions: 15
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: 394
Length of database: 395
Length adjustment: 31
Effective length of query: 363
Effective length of database: 364
Effective search space:   132132
Effective search space used:   132132
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