GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prpE in Pseudomonas fluorescens FW300-N2C3

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate AO356_16045 AO356_16045 acetyl-CoA synthetase

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_16045
          Length = 645

 Score =  814 bits (2103), Expect = 0.0
 Identities = 385/629 (61%), Positives = 483/629 (76%), Gaps = 7/629 (1%)

Query: 19  INPQQYEAMYQQSINVPDTFWGEQG-KILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNL 77
           ++  +Y+ +Y++SI  P  FW EQ  + LDW+ P+Q V+      G+ +  W+  G LN+
Sbjct: 19  LSQDEYKRLYKESIEHPSAFWAEQATRFLDWMTPWQTVQRYDLKNGDAT--WFAGGKLNV 76

Query: 78  AANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAI 137
           +ANC+DRHL   G++ AIIWEGD+ ++S  I+YK+LH  VCR AN L   G+KKGD V I
Sbjct: 77  SANCIDRHLDTRGEQVAIIWEGDNPAESAQITYKKLHNHVCRLANVLKSRGVKKGDRVCI 136

Query: 138 YMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIP 197
           YMPM+PEAA AMLAC RIGAVHSV+FGGFSP+++  RI+D++ R VIT+DEGVR GR IP
Sbjct: 137 YMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDSLRDRILDADCRTVITADEGVRGGRFIP 196

Query: 198 LKKNVDDALKN-PNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAE 256
           LK+NVD AL++ PNV++V   +V++RT G++ W EGRDLW+H  +   SD    E M+AE
Sbjct: 197 LKRNVDKALESCPNVSTV---LVVERTQGEVGWVEGRDLWYHQAMHDMSDDCPPEPMDAE 253

Query: 257 DPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYL 316
           DPLFILYTSGSTGKPKGVLHTTGGYL+ AA+TFKYV DY   +++WCTADVGWVTGHSY+
Sbjct: 254 DPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDNEVFWCTADVGWVTGHSYI 313

Query: 317 LYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTD 376
           +YGPLA GATTL+FEGVP+ P+ +R  QV+DKHQVNI YTAPTA+RALM EG   ++ T 
Sbjct: 314 VYGPLANGATTLIFEGVPSHPSSSRFWQVIDKHQVNIFYTAPTALRALMREGAGPLQETS 373

Query: 377 RSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGS 436
           R SLR+LGSVGEPINPEAWEWY+  +G ++CP+VDTWWQTETGG M++PL  A  LK G 
Sbjct: 374 RKSLRLLGSVGEPINPEAWEWYFNVVGEQRCPIVDTWWQTETGGIMLSPLVSAPRLKPGC 433

Query: 437 ATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMY 496
           ATRP FGVQP L+D  G  + GA  G L I  SWPGQ R+++GDH+R   TYF  +   Y
Sbjct: 434 ATRPMFGVQPVLLDEVGKEISGAGSGVLAIKSSWPGQIRSVYGDHQRMVDTYFKPYPGYY 493

Query: 497 FSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKG 556
           F+GDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESALV H  IAEAAVVG PH++KG
Sbjct: 494 FTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDNIAEAAVVGYPHDLKG 553

Query: 557 QAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILR 616
           Q IYA+VT  +G E + EL  E+   V KEIG  A P+++ W  +LPKTRSGKIMRRILR
Sbjct: 554 QGIYAFVTPMNGVEANDELKKELLAHVSKEIGSFAKPELIQWAPALPKTRSGKIMRRILR 613

Query: 617 KIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           KIA  +  +LGDTSTLADP VVE L++++
Sbjct: 614 KIACNELDSLGDTSTLADPSVVEGLIDKR 642


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: 1388
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: 645
Length adjustment: 38
Effective length of query: 614
Effective length of database: 607
Effective search space:   372698
Effective search space used:   372698
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.

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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:

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