Alignments for a candidate for prpE in Oleispira antarctica

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Oleispira antarctica

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_046010587.1 OLEAN_RS19275 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000967895.1:WP_046010587.1
          Length = 656

 Score =  860 bits (2223), Expect = 0.0
 Identities = 399/633 (63%), Positives = 499/633 (78%), Gaps = 5/633 (0%)

Query: 15  DRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGT 74
           ++ L+  +QY+ MYQ S+  PD FW +Q + L WI P+ KVKN SF   ++ I+W+EDG 
Sbjct: 15  EKALLTKEQYQVMYQHSLESPDEFWAQQAQRLTWITPFTKVKNVSFDKQDLHIRWFEDGF 74

Query: 75  LNLAANCLDRHLQENGDRTAIIWEGD-----DASQSKHISYKELHRDVCRFANTLLELGI 129
           LN++ NC+DRHL E G  TAI+WE D     +  +++ I+Y++L  +V R AN L  LGI
Sbjct: 75  LNVSENCIDRHLVERGHETAILWEPDGENVGEKDEARRITYQQLSSEVNRLANGLKSLGI 134

Query: 130 KKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEG 189
           KKGD+V +Y+PMVPEA +AMLACARIGAVHSV+F GFSPEA+AGRI D + R VIT+DEG
Sbjct: 135 KKGDIVTLYLPMVPEATMAMLACARIGAVHSVVFAGFSPEALAGRIEDGDCRYVITADEG 194

Query: 190 VRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQ 249
           +R G+ +PLK+NVD+A+       V +V+VL  TGG+++ Q GRD+ +HDL+ Q SD   
Sbjct: 195 LRGGKHVPLKQNVDEAIALCPAEQVNNVIVLNHTGGEVNHQVGRDIDYHDLISQQSDVCP 254

Query: 250 AEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGW 309
            E MNAEDPLFILYTSGSTGKPKGVLHTTGGYL+YA++T +YVFDY PGDIYWC ADVGW
Sbjct: 255 PEPMNAEDPLFILYTSGSTGKPKGVLHTTGGYLLYASMTHEYVFDYRPGDIYWCAADVGW 314

Query: 310 VTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGD 369
           +TGHSY++YGPL  GAT +MFEG+P +P   R A++++K+++NILY APTAIR+LMA GD
Sbjct: 315 ITGHSYIVYGPLCNGATVVMFEGIPTYPDIGRAARLIEKYKINILYVAPTAIRSLMAAGD 374

Query: 370 KAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGA 429
            A + +D SSLR+LG+VGEPINP+ W WY +  G  +CP+VDTWWQTETG  MI PLPGA
Sbjct: 375 AATKNSDLSSLRLLGTVGEPINPDVWRWYHQAFGRGECPIVDTWWQTETGAAMIAPLPGA 434

Query: 430 TELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYF 489
           T+LK GSAT P FGVQPALVD +G  L GAT G+L+I DSWPGQ R++FGDH+RF  TYF
Sbjct: 435 TDLKPGSATLPMFGVQPALVDEKGIELHGATHGNLIIKDSWPGQMRSVFGDHQRFIDTYF 494

Query: 490 STFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVG 549
           ST++  YF+GDGARRDEDGYYW+TGRVDDVLNVSGHR+GTAEIE+ALVAH  + EAAVVG
Sbjct: 495 STYEGSYFTGDGARRDEDGYYWLTGRVDDVLNVSGHRMGTAEIENALVAHDSVTEAAVVG 554

Query: 550 IPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGK 609
           +PH+IKG+ IY YVTL HG E S  L  E+  WVRKEIGP+ATPD++ W  +LPKTRSGK
Sbjct: 555 VPHDIKGEGIYVYVTLGHGFEESEALRLELIKWVRKEIGPIATPDLIQWAPALPKTRSGK 614

Query: 610 IMRRILRKIAAGDTSNLGDTSTLADPGVVEKLL 642
           IMRRILRKIA  +  ++GDTSTLADP VV+ L+
Sbjct: 615 IMRRILRKIATNEFDSIGDTSTLADPSVVDDLI 647


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: 1393
Number of extensions: 61
Number of successful extensions: 2
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: 656
Length adjustment: 38
Effective length of query: 614
Effective length of database: 618
Effective search space:   379452
Effective search space used:   379452
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)
Organisms (tab-delimited)
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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