GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Shewanella halifaxensis HAW-EB4

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_012278034.1 SHAL_RS15295 3-oxoadipyl-CoA thiolase

Query= SwissProt::P14611
         (393 letters)



>NCBI__GCF_000019185.1:WP_012278034.1
          Length = 423

 Score =  319 bits (818), Expect = 8e-92
 Identities = 178/400 (44%), Positives = 258/400 (64%), Gaps = 10/400 (2%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALER-AGVKPEQVSEVIMGQVLTA 59
           + DV I  A RT +G++G  L+ + A +L A+ IKA +ER   V  +Q  ++++G    +
Sbjct: 24  LKDVYICDAIRTPIGRYGSGLSSVRADDLAALPIKALIERNPDVDWQQCDDLLLGCANQS 83

Query: 60  GS-GQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENM 118
           G   +N AR A + AGLP  VP  T+N++CGSGL A+  AA AI  G+A++++AGG E+M
Sbjct: 84  GEDNRNIARMAGLLAGLPVEVPGCTVNRLCGSGLNALGDAARAIRTGEADLMIAGGVESM 143

Query: 119 SAAPHVLPGSRDGFRMGDAKLVDTM---IVDGLWDV-YNQYHMGITAENVAKEYGITREA 174
           S AP V+P +   F         TM    ++  +D  Y    M  TAEN+A+++ I+REA
Sbjct: 144 SRAPFVMPKATSPFARSTEFYDTTMGWRFINPEFDKHYGTEAMPQTAENLAQDFAISREA 203

Query: 175 QDEFAVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKP 234
           QD FA+ SQ KA +AQ+AG FD EIVPV IP R+G+P  F  DE +R  ++L+ +S LKP
Sbjct: 204 QDRFALWSQQKAASAQEAGLFDNEIVPVTIPVRRGEPTVFSKDEHLRL-SSLEKLSSLKP 262

Query: 235 AFDKAGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPV 294
            FDK G +TA NASG+NDGAAA+++ SA    +  L P A I   A AGV P+VMG+GPV
Sbjct: 263 LFDK-GAITAGNASGINDGAAALLLASAEGVVQHKLKPRAKILGMAVAGVPPRVMGLGPV 321

Query: 295 PASKRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGW--DTSKVNVNGGAIAIGHPIG 352
           PA+ + L R   +  D+DL+E NEAFAAQAL   +++G   D  ++N  GGAIA+GHP+G
Sbjct: 322 PATNKLLKRLNLSLDDMDLLEFNEAFAAQALTCIRELGLKDDDPRINPQGGAIALGHPLG 381

Query: 353 ASGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
            SG R+  T +++++R   +  L ++C+G G G+A+ +ER
Sbjct: 382 MSGARLATTAVNQLERTQGRYALCTMCVGVGQGIAMIIER 421


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: 382
Number of extensions: 17
Number of successful extensions: 6
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: 423
Length adjustment: 31
Effective length of query: 362
Effective length of database: 392
Effective search space:   141904
Effective search space used:   141904
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