GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Desulfatibacillum aliphaticivorans DSM 15576

Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate WP_248635324.1 G491_RS0106115 AMP-binding protein

Query= SwissProt::Q53FZ2
         (586 letters)



>NCBI__GCF_000429905.1:WP_248635324.1
          Length = 544

 Score =  612 bits (1579), Expect = e-180
 Identities = 289/545 (53%), Positives = 386/545 (70%), Gaps = 10/545 (1%)

Query: 39  NFSNYESMKQDFKLGIPEYFNFAKDVLDQWTDKEKAGKKPSNPAFWWINRNGEEMRWSFE 98
           N ++Y+    +FK  +PEYFNFA DV+D+W       + P   A  W++ +G E+R +F 
Sbjct: 7   NMTDYQKEYDEFKWEVPEYFNFAGDVIDKWA------QDPEKLAMLWVDDDGNEVRKTFA 60

Query: 99  ELGSLSRKFANILSEACSLQRGDRVILILPRVPEWWLANVACLRTGTVLIPGTTQLTQKD 158
           +L + S+K AN+L+ +  + +GD V+++LPR  EWW    AC+R G +L PGTTQLT KD
Sbjct: 61  QLSAASKKLANLLT-SLGVGQGDVVMVVLPRNIEWWEVFTACIRMGALLAPGTTQLTSKD 119

Query: 159 ILYRLQSSKANCIITNDVLAPAVDAVASKCENLHSKLIVSENSREGWGNLKELMKHASDS 218
           + +R   ++A+CIITN  LA   D VA +C  + SK+I++E  RE W    E ++ ASD 
Sbjct: 120 LQFRANKAEASCIITNPELAEKFDKVADECPTVKSKIIITE-PREDWTFYTEAVEAASDQ 178

Query: 219 HTCVKTKHNEIMAIFFTSGTSGYPKMTAHTHSSFGLGLSVNGRFWLDLTPSDVMWNTSDT 278
               KTK ++   ++FTSGT G+PKM  HTH+S+ +G  V G++WLDL P D+ WN SDT
Sbjct: 179 FETAKTKSSDNCLVYFTSGTVGFPKMALHTHASYPIGHQVTGKYWLDLKPEDMHWNVSDT 238

Query: 279 GWAKSAWSSVFSPWIQGACVFTHHLPRFEPTSILQTLSKYPITVFCSAPTVYRMLVQNDI 338
           GWAK+AWSS F PW  GA  F HH  RF+P   L+ L++YPIT  C APT+YRMLV  D+
Sbjct: 239 GWAKAAWSSYFGPWNMGAAQFIHHTDRFDPIKTLELLAQYPITTMCGAPTIYRMLVLQDL 298

Query: 339 TSYKFKSLKHCVSAGEPITPDVTEKWRNKTGLDIYEGYGQTETVLICGNFKGMKIKPGSM 398
             +KF +L+HCV AGEP+ P++ E W+  TG  I +GYGQTETVL+ G+F  ++ + GSM
Sbjct: 299 AKFKFPTLRHCVGAGEPLNPEIIEVWKKATGCVIRDGYGQTETVLLAGSFPCIEPRFGSM 358

Query: 399 GKPSPAFDVKIVDVNGNVLPPGQEGDIGIQVLPNRPFGLFTHYVDNPSKTASTLRGNFYI 458
           G+P+P  ++K++D + N LPP  EGDI I+V PNRP GLF  Y   P +TAS  RG++Y+
Sbjct: 359 GRPTPGIELKVIDEDCNELPPNTEGDIAIKVKPNRPVGLFKEYWKEPDRTASVYRGDYYL 418

Query: 459 TGDRGYMDKDGYFWFVARADDVILSSGYRIGPFEVENALNEHPSVAESAVVSSPDPIRGE 518
           TGDR Y+D+DGYFWFV RADDVIL+SGYRIGPFEVE+AL EHP+VAESAVVSSPD  RGE
Sbjct: 419 TGDRAYVDEDGYFWFVGRADDVILTSGYRIGPFEVESALIEHPAVAESAVVSSPDETRGE 478

Query: 519 VVKAFVVLNPDYKSHDQEQLIKEIQEHVKKTTAPYKYPRKVEFIQELPKTISGKTKRNEL 578
           VVKAFV+L   + + D  +L KE+QEHVK  TAPYKYPRK+EF+  LPKT+SGK +R +L
Sbjct: 479 VVKAFVILAGGFTASD--ELAKELQEHVKNVTAPYKYPRKIEFVDVLPKTVSGKIRRVQL 536

Query: 579 RKKEW 583
           R +EW
Sbjct: 537 RNQEW 541


Lambda     K      H
   0.318    0.134    0.416 

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: 927
Number of extensions: 39
Number of successful extensions: 6
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: 586
Length of database: 544
Length adjustment: 36
Effective length of query: 550
Effective length of database: 508
Effective search space:   279400
Effective search space used:   279400
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

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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:

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