GapMind for Amino acid biosynthesis

 

Alignments 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)



>FitnessBrowser__Marino:GFF832
          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 Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

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:

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. 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:

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:

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