Alignments for a candidate for prpE in Leptospirillum ferrooxidans C2-3

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Leptospirillum ferrooxidans C2-3

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_014448327.1 LFE_RS00515 acetate--CoA ligase

Query= SwissProt::P31638
         (660 letters)



>NCBI__GCF_000284315.1:WP_014448327.1
          Length = 634

 Score =  525 bits (1351), Expect = e-153
 Identities = 280/623 (44%), Positives = 404/623 (64%), Gaps = 25/623 (4%)

Query: 32  YQALCDEAERDYEGFWARHARELLHWTKPFTKVLDQSNAPFY-KWFEDGELNASYNCLDR 90
           YQ + DE+ RD E FW + A +   W++ + +VLD +   +  +WF     N + N LDR
Sbjct: 32  YQTIYDESIRDPEQFWGKIAEDF-RWSRKWDRVLDWNPKTYEARWFSGSLSNITTNMLDR 90

Query: 91  NLQNGNADKVAIVFEADDGSVTRVTYRELHGKVCRFANGLKALGIRKGDRVVIYMPMSVE 150
           ++  G ++KVA++  ADDGS    TY  +  +  R  +    +G++KGDRV I++P + E
Sbjct: 91  HIDEGLSNKVALIAVADDGSERVYTYGRIMDETNRLCHSFAEMGLKKGDRVTIFLPPTPE 150

Query: 151 GVVAMQACARLGATHSVVFGGFSAKSLQERLVDVGAVALITADEQMRGGKALPLKAIADD 210
            V++M ACAR G  H+VVF GFSA +L+ R+ D     LITAD   R GK + L   A +
Sbjct: 151 QVISMIACARSGLVHTVVFSGFSAGALKSRMEDSEPRLLITADCAYRRGKRIALLDTARE 210

Query: 211 ALALGGCEAVRNVIVYRRTGGKVAWTEGRDRW----MEDVSAGQPDTCEAEPVSAEHPLF 266
           A       ++   IV RR    +    G   +     +  S+G     +A   + + PLF
Sbjct: 211 AKK--AITSLEKTIVIRRENPDLELETGEIPFDSLLKKHASSG---FFKAVDCTTDDPLF 265

Query: 267 VLYTSGSTGKPKGVQHSTGGYLLWALMTMKWTFDIKPDDLFWCTADIGWVTGHTYIAYGP 326
           +LYTSG+TGKPKG+ H+  GY++   +T +W F+I  DD+F+C AD GW+TGH+YI YGP
Sbjct: 266 ILYTSGTTGKPKGIVHTHPGYMVGTFLTTRWVFNIHNDDVFFCVADPGWITGHSYIVYGP 325

Query: 327 LAAGATQVVFEGVPTYPNAGRFWDMIARHKVSIFYTAPTAIRSLIKAAEADEKIHPKQYD 386
           L  GAT ++ EG P YP+ GR+W ++ +++V++FY+ PTAIR  ++      K  P++YD
Sbjct: 326 LLNGATVLLAEGSPDYPDPGRWWHLVEKYRVTVFYSTPTAIRLQMRLG----KQWPEKYD 381

Query: 387 LSSLRLLGTVGEPINPEAWMWYYKNIGNERCPIVDTFWQTETGGHMITPLPGATPLVPGS 446
           LSSLRLLG+VGEPINPEAW+W ++ +   R PI+DT+WQTETG HMITPLPG  PLVPGS
Sbjct: 382 LSSLRLLGSVGEPINPEAWLW-FREVTGGRLPIMDTWWQTETGMHMITPLPG-VPLVPGS 439

Query: 447 CTLPLPGIMAAIVDETGHDVPNGNGGILVVKRPWPAMIRTIWGDPERFRKSYFPEELGGK 506
            T P PG++A +V+  G  V  G  G ++V++PWP+M RT++GDPER+RK +  EE+ G 
Sbjct: 440 ATRPFPGVVADVVNRQGESVAPGEAGFVIVRQPWPSMFRTVYGDPERYRKYW--EEIPG- 496

Query: 507 LYLAGDGSIRDKDTGYFTIMGRIDDVLNVSGHRMGTMEIESALVSNPLVAEAAVVGRPDD 566
           +Y +GD + RD   G F ++GR+DDV+ V+GHR+GT E+ESALVS+P V+EAAV+G+PD+
Sbjct: 497 VYFSGDSAKRDHH-GLFHMIGRVDDVIKVAGHRLGTAEVESALVSHPCVSEAAVIGKPDE 555

Query: 567 MTGEAICAFVVLKRSRPTGEEAVKIATELRNWVGKEIGPIAKPKDIRFGDNLPKTRSGKI 626
           + GE I AFV+L++     E    +   +R  V +E+G IA P +I   + LP+TRSGKI
Sbjct: 556 LKGEVIKAFVILRKD---AERTPDLELRIRQHVREELGAIAMPDEIEITEWLPRTRSGKI 612

Query: 627 MRRLLRSLAKGEEITQDTSTLEN 649
           MRR+L++   G     DTSTLE+
Sbjct: 613 MRRVLKARELGLP-EGDTSTLED 634


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: 1241
Number of extensions: 61
Number of successful extensions: 9
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: 634
Length adjustment: 38
Effective length of query: 622
Effective length of database: 596
Effective search space:   370712
Effective search space used:   370712
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 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