Alignments for a candidate for aacS in Halioglobus japonicus S1-36

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Halioglobus japonicus S1-36

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_102106290.1 C0029_RS07560 AMP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>NCBI__GCF_002869505.1:WP_102106290.1
          Length = 526

 Score =  280 bits (716), Expect = 1e-79
 Identities = 177/508 (34%), Positives = 256/508 (50%), Gaps = 25/508 (4%)

Query: 58  TYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRT 117
           +Y QL         A +  GL  GDR+ IW+ N  +W++  +    VG VLV +N   + 
Sbjct: 36  SYTQLDEARIAAGRAFIAAGLGKGDRIAIWAPNIYQWIIAAIGAQSVGGVLVPLNTRMKG 95

Query: 118 AEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWID 177
           AE  Y L   G KLL     F   D+LG+            P  LQ   LP L+ VV +D
Sbjct: 96  AEAAYVLQASGAKLL-----FTVGDFLGV----------NYPALLQEQALPALEQVVMLD 140

Query: 178 DEAGQGADEPGLLRFTELIARGNA-ADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATL 236
                G D  G + +   +A G++ A   +A  A  L   D ++I FTSGTTG PKG   
Sbjct: 141 -----GGD--GGVSWEIFLAEGDSVAAQEVAARADELTPDDVLDILFTSGTTGNPKGVVT 193

Query: 237 THRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPL 296
            H   +         + L   D   +  P +H FG   G LAC   GA ++ P   FD  
Sbjct: 194 CHGQNIRTFENWSATVGLRADDNYLVINPFFHSFGYKAGWLACIIRGAHML-PVKNFDLD 252

Query: 297 TVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQM 356
            V+  +  ER + + G PT++ + L HP+ A+++LS+LR  +   +P P  +++++ E +
Sbjct: 253 AVMAQIARERISMIPGPPTIYQSLLAHPQRADYDLSSLRLAVTGAAPVPVSLVEQMREAL 312

Query: 357 NLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRG 416
               +  AYG+TE+  V      D    +   + G+    +E+K VD   G  V  GQ G
Sbjct: 313 GFEVVVTAYGLTESCGVVSICRADDSAERISHSSGKAMDGVEMKCVDA-AGTTVAAGQEG 371

Query: 417 EFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGEN 476
           E   +G++VM GY  +  +T + +   GW+ TGD+  MDAEGYV I  RIKDM I GG N
Sbjct: 372 EIWFRGFNVMRGYLDNPEETAKTVTVDGWLKTGDVGVMDAEGYVRITDRIKDMFIVGGFN 431

Query: 477 IYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAH 536
            YP EIE  L   P V    V+GVPD++ GE   A+I+ + G    E  + A+ + Q+A+
Sbjct: 432 TYPAEIENILCGMPGVARAAVIGVPDERMGEVARAYIVREAGADLDEAAVIAWSREQMAN 491

Query: 537 YKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           YKVPR + F+  FPM   GKI K  +RD
Sbjct: 492 YKVPRSVGFLDEFPMNAGGKILKNNLRD 519


Lambda     K      H
   0.320    0.136    0.412 

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: 652
Number of extensions: 28
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: 578
Length of database: 526
Length adjustment: 36
Effective length of query: 542
Effective length of database: 490
Effective search space:   265580
Effective search space used:   265580
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources