Alignments for a candidate for prpE in Billgrantia desiderata SP1

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Billgrantia desiderata SP1

Align Acetate--CoA ligase CCL3; HlCCL3; 2-methylbutanoate--CoA ligase CCL4; 2-methylpropanoate--CoA ligase CCL4; Butanoate--CoA ligase CCL3; Hexanoate--CoA ligase CCL3; Isovalerate--CoA ligase CCL3; Pentanoate--CoA ligase CCL3; Propionate--CoA ligase CCL3; EC 6.2.1.1; EC 6.2.1.-; EC 6.2.1.17 (characterized)
to candidate WP_086511178.1 BZY95_RS17500 acyl-CoA synthetase

Query= SwissProt::M4IS88
         (568 letters)



>NCBI__GCF_002151265.1:WP_086511178.1
          Length = 543

 Score =  593 bits (1530), Expect = e-174
 Identities = 295/549 (53%), Positives = 381/549 (69%), Gaps = 16/549 (2%)

Query: 10  DLPKNAANYTALTPLWFLERAATVHPTRTSVIHGSRHYTWLQTYHRCRQFASALNNHSIG 69
           DLPK  AN+ AL+PL F+ER+A+++P   +VIHG    +W +T+ RCR+ ASAL    I 
Sbjct: 9   DLPKTQANHVALSPLTFIERSASIYPDYPAVIHGDIRRSWRETWARCRRLASALEKRGIK 68

Query: 70  LGSTVAVIAPNVPALYEAHFAVPMAGAVVNCVNIRLNASTIAFLLGHSSAAAVMVDQEFF 129
            G TVA + PNVPA++EAHF VP+AG V+N +NIRL+A  IA++L H  A AV+VD EF 
Sbjct: 69  PGETVAAMLPNVPAMFEAHFGVPLAGCVLNTLNIRLDAEAIAYMLEHGEAQAVLVDPEFA 128

Query: 130 SLAEEALKILAQESKSHYKPPLLVVIGDESCDPKTLEYALKTGAIEYEKFLEGGDPEFDW 189
            + E+A+  LA +       PL++ + D   + +T       G +EYE  L  GDPE+ +
Sbjct: 129 GVIEDAVSRLAIK-------PLVIDVDDALYEGETRHI----GELEYEALLAEGDPEYAY 177

Query: 190 KPPEDEWQSISLGYTSGTTASPKGVVLSHRGAYLMSLSASVVWGINEGAIYLWTLPMFHC 249
           + PEDEWQ+ISL YTSGTT  PKGVV  HRGAYL ++S  + W +    +YLWTLPMFHC
Sbjct: 178 QLPEDEWQAISLNYTSGTTGKPKGVVYHHRGAYLNAVSNILEWAMPHHPVYLWTLPMFHC 237

Query: 250 NGWCYTWGMAAFCGTNICLRQVTAKGVYSAIAKYGVTHFCAAPVVLNTIVNAPPEEAIIP 309
           NGWC+ W +AA  G ++CLR+V  K +   I    VTHF  AP+VLN +VN P E+    
Sbjct: 238 NGWCFPWTIAANAGVSVCLRRVDPKKIMDLIVDEKVTHFSGAPIVLNGLVNLPAEQKRA- 296

Query: 310 LPHLVHVMTAGAAPPPSVLFAMSEKGFKVAHTYGLSETYGPSTICAWKPEWDSLPPIKQA 369
             H V V TAGAAPP SV+  + + G +V H YGL+E YGP T+CAW+  WD LP  ++A
Sbjct: 297 FDHPVKVTTAGAAPPASVIAGVEKLGIEVTHVYGLTEVYGPVTVCAWREAWDELPLEERA 356

Query: 370 RLNARQGVRYIALEGLDVVDTKTMKPVPADGTTMGEIVMRGNAVMKGYLKNPKANEESFA 429
           R+ ARQGVRY  LE L V D  T++PVP DG T+GEI+MRGN VMKGYLKN  A E++  
Sbjct: 357 RIKARQGVRYHMLEALCVADPNTLEPVPKDGETIGEILMRGNNVMKGYLKNEAATEQALE 416

Query: 430 DGWFHSGDLAVKHPDGYIEIKDRSKDIIISGGENISSLEVENTLYLHPAVLEVSVVARPD 489
            GW+H+GDLAV HPDGYIEIKDRSKDIIISGGENIS++EVE+ +Y HPAV E +VVA+PD
Sbjct: 417 GGWYHTGDLAVWHPDGYIEIKDRSKDIIISGGENISTIEVEDAIYSHPAVEEAAVVAKPD 476

Query: 490 ERWGESPCAFVTLKPNIDKSNEQVLAEDIIKFCKSKMPAYWVPKSVVFGPLPKTATGKIQ 549
           E+WGE+PCAFV LK        +V   DII+ C+  +  + VPK+V+F  LPKT+TGKIQ
Sbjct: 477 EKWGETPCAFVKLKVGYG----EVTEADIIEHCRQHLARFKVPKTVIFTELPKTSTGKIQ 532

Query: 550 KHVLRAKAK 558
           K VLR +A+
Sbjct: 533 KFVLREEAR 541


Lambda     K      H
   0.318    0.134    0.415 

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: 925
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: 568
Length of database: 543
Length adjustment: 36
Effective length of query: 532
Effective length of database: 507
Effective search space:   269724
Effective search space used:   269724
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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Protein sequences (fasta format)
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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
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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 Amino acid biosynthesis