Aligments for a candidate for aacS in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for aacS in Pseudomonas simiae WCS417

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF2964 PS417_15170 long-chain fatty acid--CoA ligase

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



>lcl|FitnessBrowser__WCS417:GFF2964 PS417_15170 long-chain fatty
           acid--CoA ligase
          Length = 567

 Score =  232 bits (591), Expect = 3e-65
 Identities = 168/556 (30%), Positives = 264/556 (47%), Gaps = 28/556 (5%)

Query: 20  GATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLT 79
           G  D P + +     F + + +  ER A VS+  G   TYA  Q +    A+ L G G+ 
Sbjct: 28  GIEDYPSLREV----FLEHLEKFRERVAYVSI--GTEMTYADWQVQGVAFAAWLQGQGVR 81

Query: 80  PGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFK 139
            G+RV +   N  ++ +  L T   G V+VN+NP Y + E+++ L   G + +V    F 
Sbjct: 82  KGERVALMMPNCLQYPICLLGTILAGAVVVNVNPLYTSHELKHLLKDSGAETVVIFENFA 141

Query: 140 -TSDYL---GMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
            T + +     ++ +     G   G  + A +  +   V    +     + PG +RF ++
Sbjct: 142 HTLEKVITGSSVKRVVIAAIGDLLGTFKGAAMNFILRRV---QKQVPAFNLPGSVRFNQV 198

Query: 196 IARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGF----FIGEC 251
           + +G A +    ++     A     +Q+T GTTG  KG  L+HRNI+ N      ++G+ 
Sbjct: 199 LKQGRALNHFPVEMHLDALAF----LQYTGGTTGDAKGVMLSHRNIIANLLQAKAWVGDQ 254

Query: 252 MKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLH 311
           +     +     +PLYH F + +  L     G   +   +  D   V   ++ ER  G+ 
Sbjct: 255 LDQDKQETNVTLLPLYHIFSLTVNCLMFMCLGGRNILIANPRDVKRVQMILRKERFNGIA 314

Query: 312 GVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETS 371
           GV T+F   L++  F   + S LR  I  G    T V KR  E   L  I   YG+TE S
Sbjct: 315 GVNTLFNGLLENEAFCARDFSDLRMVIAGGMATHTAVAKRWKEVTGL-PIIEGYGLTECS 373

Query: 372 PVSCQSSTDTPLSKRVSTVGQVQ---PHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHG 428
           PV   S  D    + +   G +    P   V+ V  D G +  IG++GE   +G  VM G
Sbjct: 374 PVVSISPIDIARMREMEFTGSIGVPLPSTWVRFVRED-GELAEIGEQGELQVRGPQVMQG 432

Query: 429 YWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYR 488
           YW     T E +D  GW+ TGD+  MDA GY+ +V R KDM++  G N+YP EIE+ +  
Sbjct: 433 YWQRPEATAEVLDAEGWLSTGDIGVMDARGYIRLVDRKKDMILVSGFNVYPNEIEDVVAL 492

Query: 489 HPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRF-VT 547
           HP V +V  +GV D   GE++   I+ +     T++ I A C+  +  YK+P+Y+ F  T
Sbjct: 493 HPAVAEVAAIGVEDGVTGEKV-KIIVVRKDPNLTQEQILAHCREYLTGYKMPKYVEFRTT 551

Query: 548 SFPMTVTGKIQKFKIR 563
             P T  GK+ +  +R
Sbjct: 552 ELPKTTVGKVLRRALR 567


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: 716
Number of extensions: 30
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 578
Length of database: 567
Length adjustment: 36
Effective length of query: 542
Effective length of database: 531
Effective search space:   287802
Effective search space used:   287802
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 17 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 preprint on GapMind for carbon sources, or view the source code.

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