GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoB in Marinobacter adhaerens HP15

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate GFF2479 HP15_2423 acyl-CoA thiolase

Query= reanno::pseudo3_N2E3:AO353_25685
         (397 letters)



>FitnessBrowser__Marino:GFF2479
          Length = 379

 Score =  447 bits (1149), Expect = e-130
 Identities = 231/380 (60%), Positives = 290/380 (76%), Gaps = 2/380 (0%)

Query: 18  MGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGLGQAPARQAALGA 77
           MGGFQG L S+SA  LGA  I  AV RAG+    V+EV+ G VL AGL Q PARQA   A
Sbjct: 1   MGGFQGSLASVSATDLGAITIAEAVRRAGLQPADVQEVIMGNVLPAGLKQGPARQAMRKA 60

Query: 78  GLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPYLLDRARSGYR 137
           GL   T  TT+NK+CGSGM+AA+ AHD++ AGS D++VAGGMESMSNAPY+L   RSGYR
Sbjct: 61  GLPDHTGATTINKLCGSGMKAAMFAHDLIKAGSNDIMVAGGMESMSNAPYILQGVRSGYR 120

Query: 138 MGHGKV-LDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAIASTTRAQQAIK 196
           MG G+   DHMFLDGLEDA + GRLMG FA++ A+  G+TRE  DE+AI S TRA++AI+
Sbjct: 121 MGPGQAPQDHMFLDGLEDA-ETGRLMGAFAQEMADKKGYTREEMDEYAITSLTRAKKAIE 179

Query: 197 DGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTVTAANSSSISDG 256
           +G    EI+P+ V   K + ++ DDEQP  A +DKI SL+PAF   GTVTAAN+SSISDG
Sbjct: 180 EGLLKDEIIPVTVKSRKGEVVVEDDEQPHNANIDKIPSLRPAFAKDGTVTAANASSISDG 239

Query: 257 AAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLKKTGWSLDEVEL 316
           A+ALLLMR SEAEKRGLKPLA I GH+  +  P  F  APVGAI+ L  KTGWS D+V+L
Sbjct: 240 ASALLLMRESEAEKRGLKPLARIVGHSTQSQHPSEFTCAPVGAIETLFGKTGWSKDDVDL 299

Query: 317 FEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTLLSALRQKGLKR 376
           FE+NEAFA+V+++ + +L +   KVN+HGGACA GHP+G++G+R+LVTL+ AL++ G K+
Sbjct: 300 FEINEAFAMVAMMPIRELGLDPEKVNIHGGACAQGHPVGSTGSRLLVTLMYALQRYGKKK 359

Query: 377 GVAAICIGGGEATAMAVECL 396
           G+AA+CIGGGEATAMA+E L
Sbjct: 360 GIAALCIGGGEATAMAIEML 379


Lambda     K      H
   0.318    0.133    0.378 

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: 437
Number of extensions: 13
Number of successful extensions: 3
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: 397
Length of database: 379
Length adjustment: 30
Effective length of query: 367
Effective length of database: 349
Effective search space:   128083
Effective search space used:   128083
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