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_026939495.1 G415_RS0100985 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000420385.1:WP_026939495.1
          Length = 656

 Score =  607 bits (1565), Expect = e-178
 Identities = 306/648 (47%), Positives = 437/648 (67%), Gaps = 17/648 (2%)

Query: 17  PEGFASQAAIPSMEAYQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQSNAPFYKWF 76
           P  F S+A +   + Y  LC  AE D+EGFW   A+  + W +P+ KV D SNAPFYK+F
Sbjct: 9   PRDFLSKANL-KYDEYVKLCKWAEDDFEGFWDYFAKREISWFEPYKKVFDDSNAPFYKFF 67

Query: 77  EDGELNASYNCLDRNLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLKALGIR 136
             G+LN  YNC+DR++     ++ AI++E++ G    +TYREL  +V +FAN LK LG++
Sbjct: 68  VGGKLNMCYNCVDRHVTTRKKNRAAIIWESEQGESRILTYRELQYQVNKFANVLKTLGVK 127

Query: 137 KGDRVVIYMPMSVEGVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALITADEQM 196
           KGD VVIYMPM  E  +AM ACA++GA HSVVF G SA +L ER+ D  +  ++TAD   
Sbjct: 128 KGDVVVIYMPMIPELPIAMLACAKIGAIHSVVFAGMSAVALNERIKDAKSSVIVTADGGF 187

Query: 197 RGGKALPLKAIADDALALGGCEAVRNVIVYRRTGGKVAWTEGRDRWMEDVSAGQPD---- 252
           R GK +PLK   D A+     + V+ V+V R     ++    RD W +D+ +  PD    
Sbjct: 188 RAGKTIPLKENVDKAVE--KLKFVKYVVVVRHADRDISMKTLRDFWWQDLMS-DPDYAKP 244

Query: 253 TCEAEPVSAEHPLFVLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTAD 312
            CE EP+ AE PLF++YTSGST KPKGV H+T GYLLW ++T +W FD+K +D FW TA+
Sbjct: 245 YCEPEPMDAEDPLFLIYTSGSTAKPKGVVHTTAGYLLWRILTARWVFDLKEEDTFWSTAN 304

Query: 313 IGWVTGHTYIAYGPLAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIK 372
           IGW++GH+Y  YGPL+ G+T  ++EG+P YP   ++W ++ ++K+++ YTAPTAIR+L++
Sbjct: 305 IGWISGHSYTLYGPLSIGSTTFIYEGMPLYPTPAQWWYLVEKYKINVMYTAPTAIRALMR 364

Query: 373 AAEADEKIHPKQYDLSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGHM 432
             E       K+YDLSSLRLL T GE +N  AW+WY++++G +RCP++D + QTET GHM
Sbjct: 365 RGEE----WLKKYDLSSLRLLTTGGERLNEAAWLWYWEHVGGKRCPVIDAYGQTETAGHM 420

Query: 433 ITPLPGATPLVPGSCTLPLPGIMAAIVDETGHDVPN-GNGGILVVKRPWPAMIRTIWGDP 491
           I+ LP      PGS  + +PGI   IVD+ G+ +      G LV+K+PWP+M+RT+W D 
Sbjct: 421 ISALP-VVDQKPGSVGIAVPGIFPDIVDDDGNIITEPDKTGHLVLKKPWPSMVRTLWNDD 479

Query: 492 ERFRKSYFPEELGGKLYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALVS 551
           E +++ Y+  +  GK Y  GD + +D+D GYF + GR DDV+NVS HR+G  EIESAL S
Sbjct: 480 EGYKELYW-GKFNGKYYYTGDLAYKDED-GYFWMEGRADDVVNVSAHRIGCAEIESALTS 537

Query: 552 NPLVAEAAVVGRPDDMTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPKD 611
              VAEAA+VGRP+++TGE + AFVVLK          +I   LR +V + + PIAKP +
Sbjct: 538 CKYVAEAAIVGRPNEITGEEVFAFVVLKEGVDKTRHD-EIVRRLREYVEEMVSPIAKPSE 596

Query: 612 IRFGDNLPKTRSGKIMRRLLRSLAKGEEITQDTSTLENPAILEQLKQA 659
           + F D LPKTRSGK++RR+L+++A G+ I QD STLE+ ++++++K+A
Sbjct: 597 VVFVDALPKTRSGKVVRRILKAIASGKPIEQDLSTLEDISVIDRIKKA 644


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: 1290
Number of extensions: 76
Number of successful extensions: 8
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: 656
Length adjustment: 38
Effective length of query: 622
Effective length of database: 618
Effective search space:   384396
Effective search space used:   384396
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