GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Frischella perrara PEB0191

Align acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized)
to candidate WP_039104024.1 FPB0191_RS03365 acetyl-CoA C-acyltransferase

Query= ecocyc::ACETYL-COA-ACETYLTRANSFER-MONOMER
         (394 letters)



>NCBI__GCF_000807275.1:WP_039104024.1
          Length = 392

 Score =  429 bits (1102), Expect = e-125
 Identities = 226/392 (57%), Positives = 284/392 (72%), Gaps = 1/392 (0%)

Query: 1   MKNCVIVSAVRTAIGSFNGSLASTSAIDLGATVIKAAIERAKIDSQHVDEVIMGNVLQAG 60
           MK  VIVSA RTAIG FNGS+AS  AI+LG  VI+ A++R ++D+  VDEVI+GNV+Q+G
Sbjct: 1   MKKVVIVSATRTAIGHFNGSIASIDAIELGKIVIEDALKRIELDTSFVDEVIIGNVIQSG 60

Query: 61  LGQNPARQALLKSGLAETVCGFTVNKVCGSGLKSVALAAQAIQAGQAQSIVAGGMENMSL 120
           LGQNPARQ+ LK+ L+  +  FT+NKVCGSGLK++ LAAQ+I AG    ++AGGMENMS 
Sbjct: 61  LGQNPARQSALKANLSNNIPAFTINKVCGSGLKAITLAAQSILAGDNHIMIAGGMENMSQ 120

Query: 121 APYLLDAKARSGYRLGDGQVYDVILRDGLMCATHGYHMGITAENVAKEYGITREMQDELA 180
           APYL++ K R     G  Q+YD ++ DGL C+ + YHMG+TAE +AK Y I+R  QD+ A
Sbjct: 121 APYLINNKCRWNLNQGKNQLYDTLVNDGLYCSINHYHMGMTAEILAKMYDISRSDQDQFA 180

Query: 181 LHSQRKAAAAIESGAFTAEIVPVNVVTRKKTFVFSQDEFPKANSTAEALGALRPAFDKAG 240
           L S + A  AI +G F  EIVP+ V T K+ ++F QD+ PK N + + L  L P F K G
Sbjct: 181 LRSHQLAQKAISNGEFIDEIVPITVKTGKEKYIFQQDQLPKFNLSLDHLSDLIPIF-KKG 239

Query: 241 TVTAGNASGINDGAAALVIMEESAALAAGLTPLARIKSYASGGVPPALMGMGPVPATQKA 300
           TVT GN S ++DGAAAL+IM E+ A   GL PLA I+SYASG V P LMG+G V AT+ A
Sbjct: 240 TVTTGNISNLSDGAAALIIMSENRAKQLGLRPLAYIRSYASGAVNPNLMGLGSVSATKLA 299

Query: 301 LQLAGLQLADIDLIEANEAFAAQFLAVGKNLGFDSEKVNVNGGAIALGHPIGASGARILV 360
           L+ A L L+DIDLIEA E FAAQFLA+   L FD  K N+ GG IALGHPIG+SGARILV
Sbjct: 300 LKKASLNLSDIDLIEAGETFAAQFLALCYELDFDLSKTNIRGGTIALGHPIGSSGARILV 359

Query: 361 TLLHAMQARDKTLGLATLCIGGGQGIAMVIER 392
           TLL+ M   DK  GLATL IGGG GI++++ER
Sbjct: 360 TLLYTMIHHDKQFGLATLGIGGGLGISIILER 391


Lambda     K      H
   0.317    0.132    0.364 

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: 354
Number of extensions: 12
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: 392
Length adjustment: 31
Effective length of query: 363
Effective length of database: 361
Effective search space:   131043
Effective search space used:   131043
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