GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Desulfovibrio vulgaris Miyazaki F

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 8501639 DvMF_2357 AMP-binding domain protein (RefSeq)

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



>FitnessBrowser__Miya:8501639
          Length = 550

 Score =  521 bits (1343), Expect = e-152
 Identities = 265/550 (48%), Positives = 361/550 (65%), Gaps = 8/550 (1%)

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

Query: 88  SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGML 147
           + N   WV +Q ATA++G +L+ +N  YR  E+ Y L +  C+ L  +  F+  DY+  +
Sbjct: 68  ATNVPYWVALQFATAKMGAILLTVNTNYREHEIRYLLTQSECENLFIIDGFRDHDYVQTI 127

Query: 148 RELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGA-DEPGLLRFTELIARGNAADPRL 206
             + PE + Q  G L+ + LP LK V+++  E  +G    P ++  + +++     D   
Sbjct: 128 YNMIPELKTQPRGQLRCSSLPHLKRVMFLGAEKHRGMYSVPEIISMSAMVS-----DEEY 182

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

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

Query: 327 AEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKR 386
             F+ S+LRTGIMAGS CP  +M+RVVE+M +REITI YG+TE SPV  QS    P  +R
Sbjct: 302 ERFDFSSLRTGIMAGSVCPEPLMRRVVEKMYMREITICYGLTEGSPVMTQSLVTDPFERR 361

Query: 387 VSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWM 446
           V TVG+  P +EV+IVDPDT   VP G +GE   +GY+VM GY+     T  AID  GW+
Sbjct: 362 VQTVGRAMPCIEVRIVDPDTNEEVPRGTQGEVVCRGYNVMKGYYNMPEATTAAIDADGWL 421

Query: 447 HTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506
           H+GDL  MD EGYV I GRIKDM+IRGGENIYPREIEEFLY    VQDVQVVGV  +KYG
Sbjct: 422 HSGDLGVMDEEGYVVITGRIKDMIIRGGENIYPREIEEFLYGMDGVQDVQVVGVNSRKYG 481

Query: 507 EELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEM 566
           EE+ A+II KPG +   +D+R +C+G+IA +KVPRYI F+ ++PMT +GKIQKFK+R EM
Sbjct: 482 EEVGAFIIPKPGVEMAPEDVRDYCRGRIAWHKVPRYISFIDAYPMTASGKIQKFKLR-EM 540

Query: 567 KDQLGLEEQK 576
             +L  E  K
Sbjct: 541 AAELFPEAMK 550


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: 793
Number of extensions: 39
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.

Links

Downloads

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:

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