Alignments for a candidate for prpE in Methanospirillum stamsii Pt1

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Methanospirillum stamsii Pt1

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_109939574.1 DLD82_RS02360 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_003173335.1:WP_109939574.1
          Length = 629

 Score =  586 bits (1511), Expect = e-172
 Identities = 299/613 (48%), Positives = 418/613 (68%), Gaps = 14/613 (2%)

Query: 24  YEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANCLD 83
           Y+  Y + ++ PD FW ++ + LDWIKP+ K+++  +       +W+  G LN++ANCLD
Sbjct: 29  YKKAYAEFLSDPDGFWAKKARELDWIKPWDKIRDWEWPQA----RWFCGGKLNVSANCLD 84

Query: 84  RHLQENGDRT--AIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAIYMPM 141
           RH++ NG R   A+IW+G+   +  + +Y++L+R V RFAN L  LG+KKGD V +YMP+
Sbjct: 85  RHVK-NGRRNKLALIWKGERGKEEIY-TYRQLYRAVMRFANALKNLGVKKGDCVCLYMPL 142

Query: 142 VPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLKKN 201
           VPE  +AMLAC RIGAVHS++F GF  EA+  RI D+++++VIT+D G+R G+ IPL+  
Sbjct: 143 VPEHVIAMLACTRIGAVHSIVFAGFGAEALHTRIRDADAKVVITADVGIRRGKFIPLRSI 202

Query: 202 VDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAEDPLFI 261
           VD+A+KN    SVE +VVL R    ++     ++ ++ + E  S++   EEM++EDPLFI
Sbjct: 203 VDEAVKN--APSVEKIVVLSRERCPVELYSEMEVDFYAIQEGVSEECPPEEMDSEDPLFI 260

Query: 262 LYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLLYGPL 321
           LYTSG+TG+PKG++HTTGGYLV    T KY+FD    D++WCTAD GW+TGHSY++YGPL
Sbjct: 261 LYTSGTTGQPKGIVHTTGGYLVGTHYTSKYIFDLKENDVHWCTADTGWITGHSYIVYGPL 320

Query: 322 ACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDRSSLR 381
           + GAT ++ E   ++P P    +++++  V I YTAPTAIR  M  G++     + SSLR
Sbjct: 321 SVGATVVITETTLDYPDPGVWWKIIEEFGVTIFYTAPTAIRMFMRVGEEWPNKYNLSSLR 380

Query: 382 ILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSATRPF 441
           I+GSVGEP+NPEA+EWY++ IG  +CP++DTWWQTETG  MIT  P    +K G A  P 
Sbjct: 381 IIGSVGEPLNPEAFEWYYRVIGKNQCPILDTWWQTETGIHMIT-TPLGQPMKPGFAGVPI 439

Query: 442 FGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYFSGDG 501
            GV   +VD EG P+     G LVI + WP   RT+  + ER+ Q Y++   + Y  GD 
Sbjct: 440 PGVVADVVDKEGKPVPAGQGGLLVIKEPWPSMMRTVHKNKERYLQ-YWNQINHWYTVGDL 498

Query: 502 ARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQAIYA 561
           A RDEDGY  + GR DD++ V+GH LGTAE+ESALVAH  IAEAAV+G+P ++KGQA+ A
Sbjct: 499 AVRDEDGYIMVLGRSDDIIIVAGHNLGTAEVESALVAHEAIAEAAVIGVPDDMKGQAVKA 558

Query: 562 YVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRKIAAG 621
           +V L  G EPS +L +E+   VR  IGP+A P  + + D LPKTRSGKIMRR+L+    G
Sbjct: 559 FVVLCQGYEPSQKLISELIYHVRMTIGPIAMPSGIEFMDKLPKTRSGKIMRRVLKAKEMG 618

Query: 622 DTSNLGDTSTLAD 634
              + GD STL +
Sbjct: 619 --VDPGDISTLEE 629


Lambda     K      H
   0.317    0.135    0.421 

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: 1236
Number of extensions: 66
Number of successful extensions: 5
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: 652
Length of database: 629
Length adjustment: 38
Effective length of query: 614
Effective length of database: 591
Effective search space:   362874
Effective search space used:   362874
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: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources