GapMind for catabolism of small carbon sources

 

Aligments for a candidate for prpE in Marinobacter adhaerens HP15

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate GFF832 HP15_811 acetyl-CoA synthetase

Query= SwissProt::P27550
         (652 letters)



>lcl|FitnessBrowser__Marino:GFF832 HP15_811 acetyl-CoA synthetase
          Length = 649

 Score =  965 bits (2494), Expect = 0.0
 Identities = 452/637 (70%), Positives = 534/637 (83%), Gaps = 1/637 (0%)

Query: 7   HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66
           + +   +A + L+N +QYE MY+QS+  PDTFWGE GK L+WIKPY KVKNT++   N+S
Sbjct: 7   YPVSPEVAKQALLNREQYEEMYRQSVEDPDTFWGEHGKRLEWIKPYTKVKNTTYDYNNLS 66

Query: 67  IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLE 126
           IKW+EDG LN +ANCLDRHL++ GD+TAII+EGDD + S++++Y+ELH +  +FAN L  
Sbjct: 67  IKWFEDGQLNASANCLDRHLEKRGDQTAIIFEGDDPADSRNVTYRELHEETSKFANVLKG 126

Query: 127 LGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITS 186
           LG+KKGDVV IYMPM+ E AVAMLACARIGA+HSV+FGGFSPEA+  RI++  SR V+T+
Sbjct: 127 LGVKKGDVVTIYMPMIVETAVAMLACARIGAIHSVVFGGFSPEALGARIVNGKSRFVVTA 186

Query: 187 DEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGG-KIDWQEGRDLWWHDLVEQAS 245
           DEGVR GR IPLKKNVD ALKN +  +VE VVV+ RTG  ++ W E RD  + DL++ AS
Sbjct: 187 DEGVRGGRKIPLKKNVDAALKNEDAANVEKVVVVTRTGNSEVPWNEARDERYEDLMKSAS 246

Query: 246 DQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTA 305
              Q E MNAEDPLF+LYTSGSTG PKGVLHTTGGY+VYA++T +YVFDYH GD+YWCTA
Sbjct: 247 ADCQPEPMNAEDPLFMLYTSGSTGAPKGVLHTTGGYMVYASMTHEYVFDYHEGDVYWCTA 306

Query: 306 DVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALM 365
           D GWVTGHSY+LYGPLA GA T++FEGVPN+P  +RM QVVDKH+VNILYTAPTAIRALM
Sbjct: 307 DFGWVTGHSYILYGPLANGAITVLFEGVPNYPDSSRMGQVVDKHKVNILYTAPTAIRALM 366

Query: 366 AEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITP 425
           AEG+  + GT R SL++LGSVGEPINPEAWEWY + IGN KCP+VDTWWQTETGG +I+P
Sbjct: 367 AEGESCMNGTTRESLKLLGSVGEPINPEAWEWYHRVIGNSKCPIVDTWWQTETGGILISP 426

Query: 426 LPGATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFE 485
           LPGA +LK GSAT PFFGVQPALVDN+GN LEG TEG+LVI DSWPGQ RT++GDHERF 
Sbjct: 427 LPGAIDLKPGSATVPFFGVQPALVDNDGNILEGKTEGNLVILDSWPGQMRTIYGDHERFA 486

Query: 486 QTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEA 545
           QTYFST+K MYF+GDGARRDEDGYYWITGRVDDVLNVSGHRLGTAE+ESALV+H K+AEA
Sbjct: 487 QTYFSTYKGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEVESALVSHEKVAEA 546

Query: 546 AVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKT 605
           AVVG PH+IKGQ IY YVTL HG+EPS EL  E+  WVRKEIGP+A+PDV+ W   LPKT
Sbjct: 547 AVVGYPHDIKGQGIYVYVTLVHGQEPSDELKKELVQWVRKEIGPIASPDVIQWAPGLPKT 606

Query: 606 RSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLL 642
           RSGKIMRRILRKIAA +   LGDTSTLADPGVV+ L+
Sbjct: 607 RSGKIMRRILRKIAANEHDQLGDTSTLADPGVVDDLI 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: 1476
Number of extensions: 60
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: 649
Length adjustment: 38
Effective length of query: 614
Effective length of database: 611
Effective search space:   375154
Effective search space used:   375154
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 17 2021. The underlying query database was built on Sep 17 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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 preprint on GapMind for carbon sources, or view the source code.

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