GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Dyella japonica UNC79MFTsu3.2

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate N515DRAFT_1417 N515DRAFT_1417 long-chain acyl-CoA synthetase

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



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1417 N515DRAFT_1417
           long-chain acyl-CoA synthetase
          Length = 562

 Score =  238 bits (608), Expect = 4e-67
 Identities = 178/551 (32%), Positives = 273/551 (49%), Gaps = 33/551 (5%)

Query: 30  TIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWS 88
           ++ A   +  A+  +R A  S   G+  +Y Q+   + + A  L G + L  GDR+ I  
Sbjct: 26  SVAAVLEEAFAKFRDRPAFHSF--GKELSYGQIDELSRQFAGYLTGVLKLGKGDRIAIMM 83

Query: 89  HNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLR 148
            N  ++ +      + GLV+VN NP Y   E+++ L   G K +V +  F  +     L+
Sbjct: 84  PNVLQYPIALFGALRAGLVVVNTNPMYTARELKHQLEDAGAKAIVVLDNFAAT-----LQ 138

Query: 149 ELAPEWQGQQP-----GHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAAD 203
           ++  E + +       G L   K   +  V+    +       P  +RF + +A+G AA 
Sbjct: 139 QVVAETEVEHIVTTGIGDLLGLKGTLINFVLKHIKKMVPDYRLPHAVRFRDALAQG-AAH 197

Query: 204 PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNN----GFFIGECMKLTPADR 259
           P + +V  G    D   +Q+T GTTG  KGA L+H N++ N    G +IG   K  P + 
Sbjct: 198 P-VPKVDLGHD--DLAFLQYTGGTTGVAKGAMLSHGNMVANMLQAGAWIGTNAK--PGEE 252

Query: 260 LCIP-VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFI 318
           + I  +PLYH F +    L     G       +  D    ++ ++  R T L GV T+F 
Sbjct: 253 VIITALPLYHIFSLTANGLVFTRLGGLNWLITNPRDMPGFVKELKKSRFTALTGVNTLFN 312

Query: 319 AELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKR--VVEQMNLREITIAYGMTETSPVSCQ 376
             L+ P FAE + S L   +  G      V +R   V  + L E   AYG+TETSP +C 
Sbjct: 313 GLLNTPGFAEVDFSRLHLSLGGGMAVQRAVAERWKKVTGVTLAE---AYGLTETSPAACI 369

Query: 377 SSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKT 436
           +  D  L    S++G   P  +V I   D+  + PIG+ GE   KG  VM GYW    +T
Sbjct: 370 NPLD--LKDYNSSIGLPIPSTDVAIWSEDSQPL-PIGEVGELMVKGPQVMQGYWKRPDET 426

Query: 437 REAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQ 496
            + +   GW+HTGD+A MDA GYV IV R KDM++  G N+YP E+E+ +  HP V +V 
Sbjct: 427 AKVLGADGWLHTGDIARMDANGYVYIVDRKKDMILVSGFNVYPNEVEDIVMTHPGVAEVA 486

Query: 497 VVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGK 556
            VGVPD+  GE +  +++ K     T + ++ FC+  +  YK P+ I F  + P +  GK
Sbjct: 487 AVGVPDEHSGEVVKLFVVRK-DPNLTVEALKEFCRENLTGYKRPKLIEFRDALPKSNVGK 545

Query: 557 IQKFKIRDEMK 567
           I + ++RDE K
Sbjct: 546 ILRRELRDEKK 556


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: 769
Number of extensions: 46
Number of successful extensions: 6
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: 562
Length adjustment: 36
Effective length of query: 542
Effective length of database: 526
Effective search space:   285092
Effective search space used:   285092
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, 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