Alignments for a candidate for prpE in Dokdonella koreensis DS-123

GapMind for catabolism of small carbon sources

Alignments for a candidate for prpE in Dokdonella koreensis DS-123

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_067642555.1 I596_RS00340 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_001632775.1:WP_067642555.1
          Length = 646

 Score =  888 bits (2295), Expect = 0.0
 Identities = 416/639 (65%), Positives = 498/639 (77%)

Query: 7   HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66
           H +P   A    I+  QYE  Y +S+  P  FW   G+ LDWI PY +VK+ S+   ++ 
Sbjct: 5   HPVPDTFAAHARIDRAQYETAYAESVKDPAAFWDRIGRRLDWITPYTQVKDVSYDARDLH 64

Query: 67  IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126
           I+WY DG LN++ANCLDRHL   GD+TAIIWEGDD ++S+ +SY+ELH +VC+ AN L  
Sbjct: 65  IRWYYDGELNVSANCLDRHLAARGDKTAIIWEGDDPAESRRVSYRELHAEVCKAANLLTS 124

Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186
           LGI+K D VAIY+PM+PEAAVAMLAC RIGA+H+++F GFSP+++A RI DS  +LVIT+
Sbjct: 125 LGIRKDDRVAIYLPMIPEAAVAMLACTRIGAIHTIVFAGFSPDSLASRIADSQCKLVITA 184

Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASD 246
           DEG+R  + +PLK NVD+ALK PN  SVE V+V++RTGG ID Q  RD WWH L+     
Sbjct: 185 DEGLRGKKKVPLKANVDEALKRPNTNSVETVLVVRRTGGAIDMQVPRDRWWHALLADQPA 244

Query: 247 QHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTAD 306
            H      AE PLFILYTSGSTG PKGVLHTTGGYLVYA+ T + VFD    D+YWCTAD
Sbjct: 245 THAPVACEAEHPLFILYTSGSTGTPKGVLHTTGGYLVYASFTHEAVFDLREDDVYWCTAD 304

Query: 307 VGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMA 366
           +GWVTGHSYL+YGPLA GATT+MFEGVPN+P  +R  QVVDKH+V + YTAPTAIRALM 
Sbjct: 305 IGWVTGHSYLIYGPLANGATTVMFEGVPNFPDSSRFWQVVDKHKVTLFYTAPTAIRALMR 364

Query: 367 EGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPL 426
           EG+  +  T R+SLR+LGSVGEPINPEAWEWY++ +G+ +CP+VDTWWQTETGG +ITPL
Sbjct: 365 EGEDPVRKTSRASLRLLGSVGEPINPEAWEWYYRVVGDSRCPIVDTWWQTETGGILITPL 424

Query: 427 PGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQ 486
           PGAT+LK GSAT PFFG+ P +VD  G  LEGA EG+LV+TDSWPGQ RT++GDH+RF  
Sbjct: 425 PGATDLKPGSATLPFFGITPQIVDANGAVLEGAAEGNLVLTDSWPGQMRTVYGDHQRFID 484

Query: 487 TYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAA 546
           TYF T+   YF+GDGARRDEDGYYWITGRVDDV+NVSGHRLGTAE+ESALVAHP++AEAA
Sbjct: 485 TYFRTYPGTYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVAHPQVAEAA 544

Query: 547 VVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTR 606
           VVG PH+IKGQ IYAYVTL  G EP+  L  E+  WVRKEIGP+ATPD L W   LPKTR
Sbjct: 545 VVGCPHDIKGQGIYAYVTLKTGVEPTDALRKELVAWVRKEIGPIATPDHLQWAPGLPKTR 604

Query: 607 SGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           SGKIMRRILRKIA      LGDTSTLADP VV  L+ E+
Sbjct: 605 SGKIMRRILRKIAENQPDALGDTSTLADPSVVANLVNER 643


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: 1408
Number of extensions: 53
Number of successful extensions: 1
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: 646
Length adjustment: 38
Effective length of query: 614
Effective length of database: 608
Effective search space:   373312
Effective search space used:   373312
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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