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 Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_022669712.1 G415_RS0100980 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000420385.1:WP_022669712.1
          Length = 675

 Score =  715 bits (1846), Expect = 0.0
 Identities = 365/662 (55%), Positives = 480/662 (72%), Gaps = 18/662 (2%)

Query: 4   IESVMQEHRVFNPPEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTK 63
           IES ++E R+F P   F+ +A I + E Y+ L    E D+EGFW   A + + W K F +
Sbjct: 8   IESKLKETRIFYPSIEFSQRANIDA-EEYERLKKWVEMDWEGFWKYFALKKITWFKRFDE 66

Query: 64  VLDQSNAPFYKWFEDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKV 123
           VLD SN PFYK+F  G+LN SYNCLDR+++    +K AI++E+++G    +TY++L+ KV
Sbjct: 67  VLDDSNPPFYKFFTGGKLNVSYNCLDRHVKTWRKNKAAIIWESENGDTEVLTYQQLYIKV 126

Query: 124 CRFANGLKALGIRKGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVD 183
            +FA+ L+ LG++KGDRV+IYMPM  E  VAM A AR+GA HSVVFGGFS+++L++R+ D
Sbjct: 127 NKFASVLRTLGVKKGDRVLIYMPMIPEAAVAMLASARIGAIHSVVFGGFSSEALRDRIND 186

Query: 184 VGAVALITADEQMRGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWM 243
                ++TAD   R GKA+PLK+  D+AL  G    V  V+V R     +     RD W 
Sbjct: 187 AKPKVIVTADGSFRNGKAIPLKSKVDEALN-GVEHKVDYVVVVRHIERDIHMKPLRDFWW 245

Query: 244 EDVSAGQPD----TCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTF 299
           +D+ +  PD     CE E V +E PLF+LYTSGSTGKPKG+ HS+ GYLLW ++TMKW F
Sbjct: 246 QDLMS-DPDYASIYCEPEHVDSEDPLFILYTSGSTGKPKGIVHSSAGYLLWTMLTMKWVF 304

Query: 300 DIKPDDLFWCTADIGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSI 359
           DIK DD FWCTADIGW+TGH+Y  YGPLA GAT V++EGVPTYP   ++W+++ +H ++I
Sbjct: 305 DIKDDDTFWCTADIGWITGHSYGVYGPLAIGATTVMYEGVPTYPTPAKWWELVEKHSINI 364

Query: 360 FYTAPTAIRSLIKAAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPI 419
            YTAPTAIR+L++           ++DLSSLRLLGTVGEPINPEAW+WYY+ +GNER PI
Sbjct: 365 LYTAPTAIRALMRLGNE----WVLKHDLSSLRLLGTVGEPINPEAWIWYYQTVGNERAPI 420

Query: 420 VDTFWQTETGGHMITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPNGN-GGILVVKR 478
           VDT+WQTETGGHMIT +PGA    PGS  +PLPGI A +VD  G+ + + N GG+LV+ +
Sbjct: 421 VDTWWQTETGGHMITTVPGAQAAKPGSAGMPLPGIFADVVDMEGNPINDPNQGGLLVITK 480

Query: 479 PWPAMIRTIWGDPERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGH 538
           PWP+M+RTIWGD ++F   Y+ +      Y AGDG+ +D+D GYF IMGR+DDVLNVSGH
Sbjct: 481 PWPSMLRTIWGDDKKFIDVYWAKFKDKGYYFAGDGARKDED-GYFWIMGRVDDVLNVSGH 539

Query: 539 RMGTMEIESALVSNPLVAEAAVVGRPDDMTGEAICAFVVLKR--SRPTGEEAVKIATELR 596
           R+GTME+ESALVS+  VAEAAVVGRPDD+TGEAI AFVVLK    +   +E V+   ELR
Sbjct: 540 RIGTMEVESALVSHRNVAEAAVVGRPDDITGEAIVAFVVLKEGVDKTHHDELVR---ELR 596

Query: 597 NWVGKEIGPIAKPKDIRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQL 656
             V KEIGPIA+P++I F D LPKTRSGKIMRRLL+ +A G++I QD STLE+ ++L++L
Sbjct: 597 EHVQKEIGPIARPQEIIFTDALPKTRSGKIMRRLLKDIAAGKKIEQDISTLEDASVLDKL 656

Query: 657 KQ 658
            +
Sbjct: 657 AE 658


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: 1450
Number of extensions: 80
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: 660
Length of database: 675
Length adjustment: 38
Effective length of query: 622
Effective length of database: 637
Effective search space:   396214
Effective search space used:   396214
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: 54 (25.4 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:

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