GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Sporolactobacillus vineae SL153

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_010632021.1 RH97_RS08940 acetyl-CoA C-acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_000246965.1:WP_010632021.1
          Length = 392

 Score =  476 bits (1225), Expect = e-139
 Identities = 239/391 (61%), Positives = 301/391 (76%)

Query: 1   MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60
           M+EV I  A RT IGS+G SL  VPAVDLG TA KEA+++AGI    V+E+++GNVL +G
Sbjct: 1   MREVAIVGAARTPIGSFGGSLARVPAVDLGVTAAKEAIRRAGISGNLVDEILIGNVLSSG 60

Query: 61  LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120
           LGQN ARQ    AG+P   PA+T+N VCGSGLRTV L  Q+I  GDADVI+AGG E+MSR
Sbjct: 61  LGQNVARQIGIYAGIPESSPAITVNMVCGSGLRTVILGTQMIALGDADVILAGGTESMSR 120

Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180
           AP+L +N RWG +MG++K VDEM+ D L DAF+  HMG+TAEN+AERW ISRE QDEFAL
Sbjct: 121 APFLVHNTRWGNKMGDSKLVDEMLQDALVDAFSHDHMGVTAENVAERWGISRERQDEFAL 180

Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGT 240
            SQKKAE+A   G F  EI PV +  +K  TV+  DEHPR G TIE L+KL+P FK++GT
Sbjct: 181 NSQKKAEKAQLFGDFDAEIAPVDVPDKKKATVIRIDEHPRHGLTIEKLSKLRPVFKENGT 240

Query: 241 VTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAI 300
           VTAGN+SG+ND AA+LV+++ EKA+ LG+  L  + SY SA +DP IMGYGP  AT+ A+
Sbjct: 241 VTAGNSSGINDGAAMLVLIAREKAEALGLDVLGIVRSYASAALDPKIMGYGPVPATQKAL 300

Query: 301 EKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVT 360
           +K    + ++DL E NEAFAAQSLAV  DLK D ++ N+NGGAIALGHP+GASGARILVT
Sbjct: 301 KKVQMAIGDVDLFEINEAFAAQSLAVLDDLKIDPSRANINGGAIALGHPVGASGARILVT 360

Query: 361 LVHAMQKRDAKKGLATLCIGGGQGTAILLEK 391
           L++ M++  AK GLATLC+GGGQGTA+++E+
Sbjct: 361 LLYNMKRTGAKTGLATLCVGGGQGTALIVEQ 391


Lambda     K      H
   0.315    0.132    0.375 

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: 500
Number of extensions: 18
Number of successful extensions: 1
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: 392
Length of database: 392
Length adjustment: 31
Effective length of query: 361
Effective length of database: 361
Effective search space:   130321
Effective search space used:   130321
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.

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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