GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Marinobacter adhaerens HP15

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate GFF49 HP15_49 acetyl-CoA acetyltransferase

Query= BRENDA::Q0KAI3
         (392 letters)



>FitnessBrowser__Marino:GFF49
          Length = 391

 Score =  360 bits (924), Expect = e-104
 Identities = 205/403 (50%), Positives = 261/403 (64%), Gaps = 24/403 (5%)

Query: 1   MQQAVIVDAIRSPMGRSKPGSAFTELHATELLAQVIKGLVERNKLDPGLVDDVITGCVTQ 60
           M+  VIVDA+R+P+GR +   +   + A  L A V+  L+ RN L    +DDV+ GCVTQ
Sbjct: 1   MKDVVIVDAVRTPVGRFR--GSLAGVRADHLGALVLNELLYRNGLAAESIDDVVFGCVTQ 58

Query: 61  AGEQSAGPGRVAWLAAGFPDHVPATTIDRKCGSSQQAVHFAAQGIMAGAYDIVIACGIES 120
            GEQSA   R + L AG+P  VP  TIDRKCGS + AVH A   I AG+ +IV+A G E+
Sbjct: 59  IGEQSANIARTSLLGAGWPTSVPGLTIDRKCGSGEAAVHCAFGAIAAGSAEIVVAGGAEN 118

Query: 121 MSRVPMGSAR-IGQNPYGPSMEARYAPGLVSQGVAAELVAAKYELSRHDMDSYSARSHEL 179
           MSRVPMGS R +    +G  +  RY   + SQG AAE VA K+ L R  +D+++  SH  
Sbjct: 119 MSRVPMGSNRDLHGEAFGHLVSDRYE--MTSQGEAAERVAEKWNLDREQLDAFALESHRR 176

Query: 180 AATARESGAFRREIL----------GISTPNGLVEQDETIRPGTSVEKLGTLQASFRNDE 229
           AA A +SG F+ EI+          G     G    DETIR  TS+EKL TL+ SFR + 
Sbjct: 177 AAVAADSGYFKSEIVPVPVADYRENGAEKVEGKFAADETIRRDTSLEKLATLKTSFRKEN 236

Query: 230 LSARFPQIGWNVTAGNASQISDGASAMLLMSESMAQRLGLKPRARFVAFDVCGDDPVMML 289
                      +TAGN+SQISDG SA+LLMS  +A+ LGLKP+AR  A    G DP +ML
Sbjct: 237 ---------GRITAGNSSQISDGCSALLLMSSDVARNLGLKPKARIRAVTTVGADPTLML 287

Query: 290 TAPIPASQRAIKKSGLKLDQIDHYEINEAFACVPLAWQRALGADPARLNPRGGAIALGHP 349
           T PI A+++ + K+GL+LD+ID +EINEAFA VPLAW + +GADP RLN  GGAIALGHP
Sbjct: 288 TGPIGATRKVLAKAGLELDEIDLFEINEAFASVPLAWMKEVGADPERLNVNGGAIALGHP 347

Query: 350 LGASGVRLMTTMLHALEDSGQRYGLQSMCEAGGMANATIIERL 392
           LGASG R+MT+ML+ LE    RY LQ++C AGGM  ATIIER+
Sbjct: 348 LGASGARIMTSMLNELERRRGRYALQAICCAGGMGTATIIERI 390


Lambda     K      H
   0.318    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: 408
Number of extensions: 16
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: 392
Length of database: 391
Length adjustment: 31
Effective length of query: 361
Effective length of database: 360
Effective search space:   129960
Effective search space used:   129960
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 17 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