Alignments for a candidate for prpE in Desulfatibacillum aliphaticivorans DSM 15576

GapMind for Amino acid biosynthesis

Alignments for a candidate for prpE in Desulfatibacillum aliphaticivorans DSM 15576

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate WP_028313445.1 G491_RS0102365 acetate--CoA ligase

Query= SwissProt::P27550
         (652 letters)



>NCBI__GCF_000429905.1:WP_028313445.1
          Length = 646

 Score =  871 bits (2250), Expect = 0.0
 Identities = 402/638 (63%), Positives = 508/638 (79%), Gaps = 3/638 (0%)

Query: 8   TIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSI 67
           T+P +   R   +  +Y+ MY +S+N PD FW  + + +DW +P+ KVKN+SF  G+V I
Sbjct: 7   TVPEDWQKRAWCDDARYQKMYDESVNDPDAFWSREAQRIDWFEPFSKVKNSSFN-GDVDI 65

Query: 68  KWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLEL 127
           KW+ DG LN+A NCLDRHL++ GD+TAII+EG++    + I+Y++L+  VCRF+N L   
Sbjct: 66  KWFLDGKLNVAYNCLDRHLEKRGDQTAIIFEGNEPGVEEKITYRQLYERVCRFSNVLKSC 125

Query: 128 GIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSD 187
           G+KKGD V+IY+PM+P+ AVAMLACARIGA+HS++F GFSP+A+A RI D+   ++IT+D
Sbjct: 126 GVKKGDRVSIYLPMIPQLAVAMLACARIGAIHSIVFAGFSPDALANRITDAECTILITAD 185

Query: 188 EGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQ 247
           EG+R  ++I LK+  D+A+    +  V+  +V+K TG  +  + GRDLWWH+L  + S +
Sbjct: 186 EGLRGPKAIGLKEAADEAMDKAGM--VKKCIVVKHTGADVPMKAGRDLWWHELTAKESTE 243

Query: 248 HQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADV 307
              E M++EDPLFILYTSGSTG PKGVLHTTGGY+VY +LT +YVFDYH GDIYWCTAD+
Sbjct: 244 CPPESMDSEDPLFILYTSGSTGTPKGVLHTTGGYIVYTSLTHQYVFDYHDGDIYWCTADI 303

Query: 308 GWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAE 367
           GWVTGHSY++YGPLA GA T+MFEG+PN+P  +R  Q+ DKHQVNI YTAPT +RALM +
Sbjct: 304 GWVTGHSYIIYGPLANGAVTIMFEGIPNYPDFSRFWQICDKHQVNIFYTAPTVVRALMQQ 363

Query: 368 GDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLP 427
           GD  ++ T R+S+R+LG+VGEPINPEAW WY + +G E+CP+VDTWWQTETGG MITPLP
Sbjct: 364 GDGPVKATSRTSVRLLGTVGEPINPEAWLWYHRVVGEERCPIVDTWWQTETGGIMITPLP 423

Query: 428 GATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQT 487
           GAT LK GSATRPFFG+QPAL+D EGN LEG  EG LV+ DSWP  ART++GDH RF+ T
Sbjct: 424 GATALKPGSATRPFFGIQPALIDKEGNQLEGPGEGYLVMLDSWPALARTVYGDHRRFKST 483

Query: 488 YFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAV 547
           YF      YFSGDGARRDEDGYYWITGR+DDV+NVSGHRLGTAEIES+LVAHP ++EAAV
Sbjct: 484 YFIQCPGTYFSGDGARRDEDGYYWITGRIDDVINVSGHRLGTAEIESSLVAHPAVSEAAV 543

Query: 548 VGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRS 607
           VG PH+IKGQAIYAYVTL+ G EPS EL  E+  +VRK+IGP+ATP+VL +TDSLPKTRS
Sbjct: 544 VGFPHDIKGQAIYAYVTLSSGYEPSEELRKELSLFVRKDIGPIATPEVLQFTDSLPKTRS 603

Query: 608 GKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           GKIMRRILRK+A  +  NLGDTSTLADP VVE L++ +
Sbjct: 604 GKIMRRILRKVACNELDNLGDTSTLADPAVVEALIKNR 641


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: 1392
Number of extensions: 53
Number of successful extensions: 3
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 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