Alignments for a candidate for prpE in Salinicoccus carnicancri Crm

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Salinicoccus carnicancri Crm

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_017549306.1 C792_RS0110000 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000330705.1:WP_017549306.1
          Length = 560

 Score =  314 bits (805), Expect = 6e-90
 Identities = 200/557 (35%), Positives = 301/557 (54%), Gaps = 50/557 (8%)

Query: 77  EDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLKALGIR 136
           E G LN +Y  +DR++ +G  DK A+ +   D  ++  T+RE+  K   +A  LK  G  
Sbjct: 41  ETGRLNIAYETIDRHVDDGRGDKTALHYVNGDERIS-YTFREVKEKTDHYARILKENGAE 99

Query: 137 KGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALITADEQM 196
           KGDR+ +++P + E  +A+ +  ++GA  + +F  F   ++++R+ D     LIT  E +
Sbjct: 100 KGDRIFVFLPKTPECYIAILSVIKIGAIAAPLFEAFMEDAIRDRINDCHGSILITDKEMV 159

Query: 197 RGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSAGQPDTCEA 256
           R      + ++ +  L     EA  +     R+ G     EG   WME+           
Sbjct: 160 RRVPEADIPSL-ETILFAEDIEAAPS-----RSSG-----EGLVEWMEE----------- 197

Query: 257 EPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTADIGWV 316
                +  + + YTSGSTGKPKGV H+    +     + KW  DIK DD++WCT+  GWV
Sbjct: 198 -----DDGMLIHYTSGSTGKPKGVLHAHR-VVSHQYQSGKWVLDIKDDDVYWCTSHPGWV 251

Query: 317 TGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIKAAEA 376
           TG  Y  + P    AT V+  G      A  ++ +IA  KV+I+Y+APTA R L+   + 
Sbjct: 252 TGSVYGLFAPWLNRATVVIQGG---RFKAEHWYKLIAELKVTIWYSAPTAFRMLLSQGDI 308

Query: 377 DEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGHMITPL 436
            E      YDLSSLR + +VGEP+NPE   W ++ +G     I DT+W TETG H++  L
Sbjct: 309 LEG-----YDLSSLRHILSVGEPLNPEVIYWAWEELGVR---IHDTWWMTETGAHLVVNL 360

Query: 437 PGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGDPERFRK 496
           PG   + PGS   P PG+   I+DE G+ VP G  G L V+ PWP +++ IWG+ ++F  
Sbjct: 361 PGEK-IKPGSMGRPFPGVEVGILDEAGNVVPRGTTGQLAVRTPWPGLMKEIWGNKDKF-D 418

Query: 497 SYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPLVA 556
           SYF  E     YL+GD + +D D  Y     R DD++N SG R+G  E+ES L+ +  + 
Sbjct: 419 SYFKYE---GWYLSGDLAYQD-DEDYVFFQSRDDDMINSSGERIGPFEVESKLIEHEAIQ 474

Query: 557 EAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPKDIRFGD 616
           EA V+G+PD + GE + AF+VL   R    ++  +  E+R +V   +     PK+I   +
Sbjct: 475 EAGVIGKPDPVRGEIVKAFIVL---RDGFVQSPDLLEEIRVFVRNNLAAHVAPKEIEVME 531

Query: 617 NLPKTR-SGKIMRRLLR 632
            LPKT  SGKI+RR L+
Sbjct: 532 ELPKTTISGKILRRELK 548


Lambda     K      H
   0.319    0.136    0.422 

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: 1067
Number of extensions: 63
Number of successful extensions: 10
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: 660
Length of database: 560
Length adjustment: 37
Effective length of query: 623
Effective length of database: 523
Effective search space:   325829
Effective search space used:   325829
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 Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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 2024 update 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 original 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