GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Methanoculleus horonobensis T10

Align acetyl-CoA C-acetyltransferase (subunit 2/2) (EC 2.3.1.9) (characterized)
to candidate WP_067077233.1 MCUHO_RS09135 thiolase domain-containing protein

Query= BRENDA::I3R3D1
         (383 letters)



>NCBI__GCF_001602375.1:WP_067077233.1
          Length = 386

 Score =  289 bits (740), Expect = 8e-83
 Identities = 167/386 (43%), Positives = 229/386 (59%), Gaps = 8/386 (2%)

Query: 1   MDRVAIIGASMTQFGQRDAW---IRELLAEAGQAALADADVSPDEIEHLYVSNMASGEFE 57
           M  VA+IG   T+FG+   W    R+L  +AG  AL DA V+ ++++ LYV NM++G F 
Sbjct: 1   MRDVAVIGVGCTEFGEH--WGTSFRDLFVKAGALALEDAGVTGEKLDALYVGNMSAGRFV 58

Query: 58  GQTGVPNALAH--DLAAMPAYTARIDQTSSSGGAGVYAAWQSVASGASDMTMLVGGEKMT 115
            Q  +   +A    LA     + R++   +SGG     A  +VASG  D+ +  G EKMT
Sbjct: 59  EQEHIGALIADYAGLATNNTPSTRVEAACASGGLAFRQAVIAVASGMEDIVVAAGVEKMT 118

Query: 116 HRSTAEATDVIASLT-HPVEYKHGVTLPSFAGLTARLYLDTYDAPRESLGKVAVKNHKNG 174
              T  + D++AS      E   G T P    + A  Y+  Y   RE L +VAVKNH+NG
Sbjct: 119 DVGTGASVDMLASAADREWEGFAGATFPGLYAMIANDYMHRYPLTREQLAQVAVKNHENG 178

Query: 175 LDNPHAQFRKEVDLETVLDSPVVADPLRLYDFCPITDGSAALVFCSESVAREYTDDYVVI 234
             NP AQFR  + ++TVL+S +VADPLRL+D  PITDG+AA+V      ARE+TD  V +
Sbjct: 179 AKNPIAQFRNRITVDTVLNSSLVADPLRLFDCSPITDGAAAVVVVPLERAREFTDSPVRV 238

Query: 235 SGIGGATDTHVVHERADPTTMGGVVNSSDIAYEMADLEPDDIDVAELHDMFTILEFLQSE 294
                A+DT  +H+R + +T+   V +   A+  A L   DID+ E+HD FTI E    E
Sbjct: 239 LASAQASDTISLHDRREISTLDASVAAGKRAFAQAGLTHKDIDMVEVHDCFTIAEICAIE 298

Query: 295 DLGFFEKGEGWKAVEEGVTDRDGELPINTSGGLKSKGHPLGASGVAQVYEIYKQLIGDAG 354
           DLGF +KGE  +   +G T   GE+P+NTSGGLK+ GHP+GA+G+ Q+YEI  QL G+A 
Sbjct: 299 DLGFCKKGEAGRLTADGATALGGEIPVNTSGGLKACGHPVGATGIKQIYEIVSQLRGEAT 358

Query: 355 DRQVDADIGLACNVGGFGNCVTTTIM 380
            RQVDA+IG+A NVGG G  V   I+
Sbjct: 359 GRQVDAEIGMAHNVGGTGATVVVHIL 384


Lambda     K      H
   0.315    0.132    0.384 

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: 456
Number of extensions: 17
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: 383
Length of database: 386
Length adjustment: 30
Effective length of query: 353
Effective length of database: 356
Effective search space:   125668
Effective search space used:   125668
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: 42 (22.0 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