Alignments for a candidate for prpE in Hippea alviniae EP5-r

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Hippea alviniae EP5-r

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_022669557.1 G415_RS0100205 AMP-binding protein

Query= SwissProt::Q53FZ2
         (586 letters)



>NCBI__GCF_000420385.1:WP_022669557.1
          Length = 558

 Score =  505 bits (1300), Expect = e-147
 Identities = 258/551 (46%), Positives = 353/551 (64%), Gaps = 18/551 (3%)

Query: 39  NFSNYESMKQDFKLGIPEYFNFAKDVLDQWTDKEKAGKKPSNPAFWWINRNGEEMR-WSF 97
           N  NYE   ++FKL +PEY+NFA DV+D+W +        +  A  W +  G+ ++ ++F
Sbjct: 4   NMVNYEEEVRNFKLEVPEYYNFAFDVVDKWAEDR------TKLALVWADTTGKTIKKYTF 57

Query: 98  EELGSLSRKFANILSEACSLQRGDRVILILPRVPEWWLANVACLRTGTVLIPGTTQLTQK 157
            ++  +S KFAN+L  +  +++GD V +++PR+ EW+   +   + G V +P    L   
Sbjct: 58  WDISMMSNKFANVLL-SLGIKKGDHVFIMVPRIVEWYAVMLGLNKVGAVAMPAPNILMPD 116

Query: 158 DILYRLQSSKANCIITNDVLAPAVDAVASK--CENLHSKLIVSENSREGWGNLKELMKHA 215
           DI YR++  +A   I +   A  V+   S   C +L  K+I+ +   EGW + +  M  A
Sbjct: 117 DIRYRIRQGEAVMAIASASNASKVEQACSNGDCPSLKVKMII-DGDLEGWVSFENQMDKA 175

Query: 216 SDSHT---CVKTKHNEIMAIFFTSGTSGYPKMTAHTHSSFGLGLSVNGRFWLDLTPSDVM 272
           +D  +      TK  + + I+FTSGT+ YPKM  H   S+ L   V  ++W DL P+D+ 
Sbjct: 176 TDKLSKDDVEPTKATDPLLIYFTSGTTKYPKMVMH-EQSYALAHIVTAKYWHDLQPTDLH 234

Query: 273 WNTSDTGWAKSAWSSVFSPWIQGACVFTHHL-PRFEPTSILQTLSKYPITVFCSAPTVYR 331
           W  SDTGW K+ W  ++  W  GA VF H+    F+P   L+ L+   IT FC+ PTVYR
Sbjct: 235 WTISDTGWGKAVWGKLYGQWQIGAAVFMHNAGAHFDPKITLRLLTTQGITSFCAPPTVYR 294

Query: 332 MLVQNDITSYKFKSLKHCVSAGEPITPDVTEKWRNKTGLDIYEGYGQTETVLICGNFKGM 391
           ML+Q D++ Y F SL+HC SAGEPI P+V + W+N TG  IY+GYGQTE+VL+  N+  M
Sbjct: 295 MLIQEDLSKYDFSSLRHCTSAGEPINPEVIKAWKNATGTLIYDGYGQTESVLLVANYPCM 354

Query: 392 KIKPGSMGKPSPAFDVKIVDVNGNVLPPGQEGDIGIQVLPNRPFGLFTHYVDNPSKTAST 451
            IK GSMGKP P FDVKIVD +GN +P G+ G I +++ P  P GL   Y  + + TA  
Sbjct: 355 PIKYGSMGKPVPGFDVKIVDDDGNEMPVGEPGHIAVRIKPEHPIGLTKGYYKDEAATAEA 414

Query: 452 LRGNFYITGDRGYMDKDGYFWFVARADDVILSSGYRIGPFEVENALNEHPSVAESAVVSS 511
            RG+FY TGDR Y D DGYFWF  RADDVI SSGYRIGPFEVE+AL EHP+V ESAVV S
Sbjct: 415 FRGDFYFTGDRAYQDVDGYFWFYGRADDVIKSSGYRIGPFEVESALQEHPAVVESAVVGS 474

Query: 512 PDPIRGEVVKAFVVLNPDYKSHDQEQLIKEIQEHVKKTTAPYKYPRKVEFIQELPKTISG 571
           PDPIRG +VKAF++L   Y+    E+LI++IQ+ VKK TAPYKYPR++EF++ELPKTISG
Sbjct: 475 PDPIRGTIVKAFIILADGYE--PGEELIRDIQDFVKKKTAPYKYPREIEFVKELPKTISG 532

Query: 572 KTKRNELRKKE 582
           K KR  LR+ E
Sbjct: 533 KIKRAVLRRME 543


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: 873
Number of extensions: 41
Number of successful extensions: 7
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: 558
Length adjustment: 36
Effective length of query: 550
Effective length of database: 522
Effective search space:   287100
Effective search space used:   287100
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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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