Alignments for a candidate for acs in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for acs in Desulfovibrio vulgaris Miyazaki F

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 8501639 DvMF_2357 AMP-binding domain protein (RefSeq)

Query= metacyc::MONOMER-20125
         (556 letters)



>FitnessBrowser__Miya:8501639
          Length = 550

 Score =  175 bits (443), Expect = 5e-48
 Identities = 166/565 (29%), Positives = 252/565 (44%), Gaps = 81/565 (14%)

Query: 20  LERAATVYGDCTSVVYDAVSYTWSQTHRRCLC----LASSIASLGIENGHVVSVLAPNVP 75
           L+     Y D  +V+Y  V   + QT+R+       LA  + +LG+ +G  V+V A NVP
Sbjct: 15  LDETVAKYPDNDAVIY--VDRDYRQTYRQFSQVVDDLAKGLMALGVRHGEKVAVWATNVP 72

Query: 76  QMYELHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFV-----DHLSRDLILEAIA 130
               L FA    GAIL  VN       I  LL  SE + +F+     DH   D +     
Sbjct: 73  YWVALQFATAKMGAILLTVNTNYREHEIRYLLTQSECENLFIIDGFRDH---DYVQTIYN 129

Query: 131 LFPKQAPVPR-------------LVFMADESESGNSSE---LGKEFFCSYKDLIDRG--- 171
           + P+    PR             ++F+  E   G  S    +      S ++  +R    
Sbjct: 130 MIPELKTQPRGQLRCSSLPHLKRVMFLGAEKHRGMYSVPEIISMSAMVSDEEYAERQRAL 189

Query: 172 DPDFKWVMPKSEWDPMILNYTSGTTSSPKGVVHCH-----RGIFIMTVDSLIDWGVPKQP 226
           DP           D + + YTSGTT  PKGV+  H      G +I       +    K  
Sbjct: 190 DPH----------DVVNMQYTSGTTGFPKGVMLTHVNIGNNGYWIGKNQHFTE----KDR 235

Query: 227 VYLWTLPMFHANGWSYPWGMAAV--GGTNICLRKFDSEIIYDMIKRHGVTHMCGAP---- 280
           V L  +P+FH  G      +AA+  G   + L  F    +   + +   T + G P    
Sbjct: 236 VCL-PVPLFHCFGCVLGV-LAAINHGAALVILESFSPMHVMASVDQEKCTALYGVPTMFL 293

Query: 281 -VVLNMLSNAPGSEPLKTTVQIMTAGAPPPSAVLFRTESLGFA--VSHGYGLTETAGLVV 337
            V+ + L        L+T +    AG+  P  ++ R     +   ++  YGLTE + ++ 
Sbjct: 294 AVLEHKLFERFDFSSLRTGIM---AGSVCPEPLMRRVVEKMYMREITICYGLTEGSPVMT 350

Query: 338 SCAWKKEWNHLPATERARLKSRQGVGTVMQT-KIDVVDPVTGAAVKRDGSTLGEVVLRGG 396
                  +           +  Q VG  M   ++ +VDP T   V R   T GEVV RG 
Sbjct: 351 QSLVTDPFE----------RRVQTVGRAMPCIEVRIVDPDTNEEVPR--GTQGEVVCRGY 398

Query: 397 SVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVE 456
           +VM GY   PE T  ++ ADGW ++GD+GVM  +GY+ I  R KD+II GGEN+   E+E
Sbjct: 399 NVMKGYYNMPEATTAAIDADGWLHSGDLGVMDEEGYVVITGRIKDMIIRGGENIYPREIE 458

Query: 457 SILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPK 516
             LY    + +  VV      +GE   AF+  K G+   P  +++ +YCR ++  + VP+
Sbjct: 459 EFLYGMDGVQDVQVVGVNSRKYGEEVGAFIIPKPGVEMAP--EDVRDYCRGRIAWHKVPR 516

Query: 517 TVVFKEELPKTSTGKVQKFILRDMA 541
            + F +  P T++GK+QKF LR+MA
Sbjct: 517 YISFIDAYPMTASGKIQKFKLREMA 541


Lambda     K      H
   0.319    0.135    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: 703
Number of extensions: 36
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: 556
Length of database: 550
Length adjustment: 36
Effective length of query: 520
Effective length of database: 514
Effective search space:   267280
Effective search space used:   267280
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 (21.7 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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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