GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF2964
          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.

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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