Aligments for a candidate for aacS in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Aligments for a candidate for aacS in Desulfovibrio vulgaris Hildenborough

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 208580 DVU3065 AMP-binding enzyme family protein

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



>MicrobesOnline__882:208580
          Length = 550

 Score =  506 bits (1304), Expect = e-148
 Identities = 256/538 (47%), Positives = 352/538 (65%), Gaps = 7/538 (1%)

Query: 28  EQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIW 87
           E T+G    +  A+ P+ +A+V V +  R TY +  +    LA  L+ +G+  GD+V +W
Sbjct: 8   EMTLGRILDETAAKFPDNDAVVYVDRDYRQTYREFVSVVDDLARGLMALGVKRGDKVALW 67

Query: 88  SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGML 147
           + N   WV +Q ATA++G VL+ +N  YR +E+ Y L +  C+ L  M  F+  D++  +
Sbjct: 68  ATNVPYWVALQFATAKIGAVLLTVNTNYRESELRYLLEQSECENLFIMDGFRDHDFVQTI 127

Query: 148 RELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARG-NAADPRL 206
            ++ PE + Q  G L+   LP LK V+++  E  +G     +    E+++ G   +D   
Sbjct: 128 YQVIPELRMQPRGQLRCEGLPHLKRVMFLGAEKHRG-----MYSVPEIVSLGVMVSDEEF 182

Query: 207 AQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPL 266
            Q    L   D +N+Q+TSGTTGFPKG  LTH  I NNG++IG     T  DR+C+PVPL
Sbjct: 183 RQRQDELDPYDVVNMQYTSGTTGFPKGVMLTHVGIGNNGYWIGRNQGFTEKDRVCLPVPL 242

Query: 267 YHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRF 326
           +HCFG VLG +A   HGA +V   + F+P+ V+ +V  E+CT L+GVPTMF+A L+H  F
Sbjct: 243 FHCFGCVLGVMAAINHGAALVIL-ENFNPMHVMASVDQEKCTALYGVPTMFLAVLEHKLF 301

Query: 327 AEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKR 386
             F+ S+LRTGIMAGS CP  +M+RV+E+MN+REITI YG+TE SPV  Q+  D  L +R
Sbjct: 302 DRFDFSSLRTGIMAGSVCPEPLMRRVIEKMNMREITICYGLTEGSPVMTQTLVDDSLERR 361

Query: 387 VSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446
           V TVG+  P +EV+IVDP+T   VP G  GE   +GY+VM GY+     T +A+D  GW+
Sbjct: 362 VQTVGRAMPGIEVRIVDPETNEEVPHGTPGEVVCRGYNVMKGYYNMPEATAKAVDGDGWL 421

Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506
           H+GDL  MD  GYV I GRIKDM+IRGGENIYPREIEEFLY    VQDVQVVGVP +KYG
Sbjct: 422 HSGDLGIMDEHGYVRITGRIKDMIIRGGENIYPREIEEFLYGMEGVQDVQVVGVPSRKYG 481

Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           EE+ A+II K G     +D+R  C+G+I+ YKVPR+I FV+ FPMT + KIQK+K+R+
Sbjct: 482 EEVGAFIIPKEGYDLAPEDVRDHCRGRISWYKVPRHIAFVSEFPMTASAKIQKYKLRE 539


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: 820
Number of extensions: 43
Number of successful extensions: 3
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: 550
Length adjustment: 36
Effective length of query: 542
Effective length of database: 514
Effective search space:   278588
Effective search space used:   278588
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

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, 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