GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Kocuria flava HO-9041

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_058857116.1 AS188_RS00055 long-chain fatty acid--CoA ligase

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



>NCBI__GCF_001482365.1:WP_058857116.1
          Length = 568

 Score =  237 bits (604), Expect = 1e-66
 Identities = 179/564 (31%), Positives = 274/564 (48%), Gaps = 35/564 (6%)

Query: 23  DVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGD 82
           D+ L E ++       VAR   R AL     G R +YA+L  +  R A  L  +G+  GD
Sbjct: 26  DLELPETSLVHMLERSVARHGHRPALEFF--GARTSYARLGEQVERAAEGLRRLGVAAGD 83

Query: 83  RVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSD 142
           RV I   N  + ++   A  ++G V+V  NP Y   E+ +     G ++ +   R   +D
Sbjct: 84  RVAIVLPNCPQHIVAFYAVLRLGAVVVEHNPLYTAPELRHQFEDHGARVAIVWDR--AAD 141

Query: 143 YLGMLRE-------LAPEWQGQQPGHLQAA---KLPQLKTVVWIDDEAGQGADEPGLLRF 192
            +  L E       +A +     P   +AA    LP  +        A      PG + +
Sbjct: 142 RIRSLPEDLRLDAVVAVDVTQAMPRRTRAALRLPLPAARA-----SRAQLTGPAPGTIPW 196

Query: 193 TELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECM 252
             L+A    A+P LA       A D   +Q+TSGTTG PKGA LTHRN+ +N   +G+  
Sbjct: 197 RRLVA----AEP-LAADHPRPTAHDLALLQYTSGTTGLPKGAMLTHRNLESNAL-MGQHW 250

Query: 253 KLTPADRLCIPV-PLYHCFGMVLGNLACFTHGATIV-YPNDGFDPLTVLQTVQDERCTGL 310
             +  D +   V PL+H FG+ LG     + GA +V +P    D   VL+ ++  R T L
Sbjct: 251 LHSGEDEVVHGVLPLFHAFGLTLGVTFAMSLGARLVLFPTVRAD--LVLKALRRSRPTVL 308

Query: 311 HGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTET 370
             VP ++   LD       +L  +   +      P  +++R  E+     +   YG+TE 
Sbjct: 309 PAVPPVYEKLLDAAEERGADLRGIAVAVSGAMTLPVPLVERW-ERATGGMLVEGYGLTEC 367

Query: 371 SP-VSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGY 429
           SP V+C    D   S+R  ++G   P  E+++VDP+T   VP G  GE   +G  V  GY
Sbjct: 368 SPLVACNPLND---SRRAGSIGVPFPSTEIRLVDPETLEDVPRGHEGELWVRGPQVFRGY 424

Query: 430 WGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRH 489
           W    +T   + E GW+ TGD+ T+D +G++ +V RIK+++I GG N+ P E+E  L  H
Sbjct: 425 WKRPEETARVLVEDGWLRTGDVVTVDDDGFLRVVDRIKEVIITGGFNVAPTEVETALKLH 484

Query: 490 PQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSF 549
             V D  VVG+ D + GE + A ++  PG    E  +R  C G++  YKVPR I  V   
Sbjct: 485 DDVADAAVVGLDDGRGGEAVVAAVVLAPGAVLDEQALREHCYGKVTRYKVPRRIVAVEDL 544

Query: 550 PMTVTGKIQKFKIRDEMKDQLGLE 573
           P T+ GK  + ++R  + + LG++
Sbjct: 545 PRTMLGKTLRREVRARL-EALGVQ 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: 730
Number of extensions: 34
Number of successful extensions: 4
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: 568
Length adjustment: 36
Effective length of query: 542
Effective length of database: 532
Effective search space:   288344
Effective search space used:   288344
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.

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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