GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Rhodobacter viridis JA737

Align acetyl-CoA acetyltransferase (EC 2.3.1.16; EC 2.3.1.9) (characterized)
to candidate WP_110804969.1 C8J30_RS06880 acetyl-CoA C-acetyltransferase

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



>NCBI__GCF_003217355.1:WP_110804969.1
          Length = 403

 Score =  263 bits (671), Expect = 9e-75
 Identities = 167/418 (39%), Positives = 229/418 (54%), Gaps = 40/418 (9%)

Query: 1   MKNCVIVSAVRTAIGS--FNGSLASTSAIDLGATVIKAAIERAKIDSQHVDEVIMGNVLQ 58
           M    I  A RT  G    +GSL   +++ L A ++ A  ER  +    V++VI GNV Q
Sbjct: 1   MTEAYIYDACRTPRGKGRADGSLHEVTSVALSARLLDAVAERNGLTGHAVEDVIWGNVTQ 60

Query: 59  AG-LGQNPARQALLKSGLAETVCGFTVNKVCGSGLKSVALAAQAIQAGQAQSIVAGGMEN 117
            G  G   AR A+L SGL E++ G ++N+ C SG+++V LAA  ++AG   + +AGG+E 
Sbjct: 61  VGEQGGCLARSAVLLSGLDESIPGLSINRFCASGMEAVNLAANQVKAGAGAAYIAGGVEM 120

Query: 118 MSLAPYLLDAKARSGYRLGDGQVYDVILRDGLMCATHGYHMGITAENVAKEYGITREMQD 177
           MS      D  A             + +   L   T+    GI+A+ +A EYG TREM D
Sbjct: 121 MSRVAMGSDGAA-------------IAVDPSLAMKTYFVPQGISADVIATEYGFTREMAD 167

Query: 178 ELALHSQRKAAAAIESGAFTAEIVPVNVVTRKKTFVFSQDEFPKANSTAEALGALRPAFD 237
            LA+ SQR+AA A     F   IVPV    +    +  +DE+ +  +T E L  L+PAF 
Sbjct: 168 ALAVESQRRAAEAWAENRFAKSIVPVR--DQNGLIILERDEYLRPGTTMEDLAKLKPAFK 225

Query: 238 KAGTVT----------------------AGNASGINDGAAALVIMEESAALAAGLTPLAR 275
             G V                       AGN+SGI DGAAA++I  +    A GL P AR
Sbjct: 226 DMGEVMPGFDKVAMLKYPHLERIEHIHHAGNSSGIVDGAAAVLIGSKEFGEAHGLKPRAR 285

Query: 276 IKSYASGGVPPALMGMGPVPATQKALQLAGLQLADIDLIEANEAFAAQFLAVGKNLGFDS 335
           I++ A  G  P +M  GPVP T+K L+ +G+ ++DIDL E NEAFAA  L   +      
Sbjct: 286 IRATAKIGTDPTIMLTGPVPVTEKILRDSGMSISDIDLFEVNEAFAAVVLRFMQAFDVGQ 345

Query: 336 EKVNVNGGAIALGHPIGASGARILVTLLHAMQARDKTLGLATLCIGGGQGIAMVIERL 393
           +KVNVNGGA+ALGHP+GA+GA I+ TLL  ++ RD + GLATLCI  G G A +IER+
Sbjct: 346 DKVNVNGGAMALGHPLGATGAIIIGTLLDELERRDLSTGLATLCIASGMGAATIIERV 403


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: 414
Number of extensions: 14
Number of successful extensions: 5
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: 403
Length adjustment: 31
Effective length of query: 363
Effective length of database: 372
Effective search space:   135036
Effective search space used:   135036
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