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 8499484 DvMF_0256 AMP-dependent synthetase and ligase (RefSeq)

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



>FitnessBrowser__Miya:8499484
          Length = 583

 Score =  175 bits (443), Expect = 5e-48
 Identities = 145/542 (26%), Positives = 240/542 (44%), Gaps = 43/542 (7%)

Query: 20  LERAATVYGDCTSVVYDAVSYTWSQTHRRCLCLASSIASLGIENGHVVSVLAPNVPQMYE 79
           L+RAA      T++ +     ++++  +    +A+++ + G+  G  VS++ PN+PQ   
Sbjct: 35  LDRAAERTPRRTAIAFRNYRISYAKLRQLAEVMAANLRAQGVRRGDKVSIMLPNLPQTVI 94

Query: 80  LHFAVPMAGAILNAVNLRLDARTISILLHHSESKLIFVDHLSRDLILEAIALFPKQAPVP 139
             +AV  AG ++   N     + +   +H S ++ +    ++ DL+   I    ++  + 
Sbjct: 95  AFWAVLKAGGVVVMTNPLYMEKELVHQIHDSGARFM----IALDLVWPKIEPLREKLGID 150

Query: 140 RL-----------------VFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPKS 182
           +                   F A    +             +K L+ +G           
Sbjct: 151 KYFLTRIGDGLAFPLNFLYAFKAKREGTWRELPFDGRHVLPWKTLL-KGKVRHSTTTCNP 209

Query: 183 EWDPMILNYTSGTTSSPKGVV--HCHRGIFIMTVDSLIDWGVPKQPVYLWTLPMFHANGW 240
             D  +L YT GTT   KGV+  H +  + +  + +++         +L  +P FH  G 
Sbjct: 210 TEDLAVLQYTGGTTGISKGVMLTHHNMSVNVQQITTILGDARDMDHCFLGLMPYFHVYGL 269

Query: 241 SYPWGM-AAVGGTNICLRKFDSEIIYDMIKRHGVTHMCGAPVVLNMLSNAP--GSEPLKT 297
           +    +  A+  T +   ++    +   I++H  T   GAP +   L      G   L +
Sbjct: 270 TTCLTLPTALAATIVPFPRYVPRDVLVGIQKHKPTIFPGAPSIYISLMQQKEVGDYDLTS 329

Query: 298 TVQIMTAGAPPPSAVLFRTESL-GFAVSHGYGLTETAGLVVSCAWKKEWNHLPATERARL 356
               ++  AP P   + R   L G  V  G+GLTE + +           HL        
Sbjct: 330 IRYCISGSAPMPVEHIKRFRELTGAQVIEGFGLTEASPVT----------HLNPIHGVSK 379

Query: 357 KSRQGVGTVMQTKIDVVDPVTGAAVKRDGSTLGEVVLRGGSVMLGYLKDPEGTAKSMTAD 416
               G+     T+  +VD   G  V      +GE+++RG  VM GY   P+ TA ++  +
Sbjct: 380 TGSIGI-PFPDTEARIVDMEVGQ-VPLPAGKVGELIIRGPQVMKGYWNRPDETANTLR-N 436

Query: 417 GWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEVESILYSHPDILEAAVVARPDE 476
           GW YTGD+ +M  DGY  I DR KD+ + GG N+   E++ +L+ HP I EA  V  P  
Sbjct: 437 GWLYTGDIAIMDEDGYFTIVDRKKDMFLVGGYNVYPREIDEVLHEHPKIKEAVTVGVPHP 496

Query: 477 FWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVPKTVVFKEELPKTSTGKVQKFI 536
             GE   AFV +K G  +K T+ E+V +CR KL  Y VPK V F+++LPKT  GKV + I
Sbjct: 497 TRGEMIKAFVVVKPG--EKLTKAEVVAHCREKLASYKVPKQVEFRDDLPKTVVGKVLRRI 554

Query: 537 LR 538
           LR
Sbjct: 555 LR 556


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: 791
Number of extensions: 50
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 556
Length of database: 583
Length adjustment: 36
Effective length of query: 520
Effective length of database: 547
Effective search space:   284440
Effective search space used:   284440
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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