Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 8501039 DvMF_1775 acetate/CoA ligase (RefSeq)
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__Miya:8501039 Length = 667 Score = 745 bits (1923), Expect = 0.0 Identities = 368/626 (58%), Positives = 465/626 (74%), Gaps = 10/626 (1%) Query: 23 QYEAMYQQSINVPDTFWGEQGK-ILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLAANC 81 +Y A +++ P+ FWG++ + +LDW P+ KV + I+W++ TLN+A NC Sbjct: 39 EYLAHRERADKDPEGFWGDRARQLLDWFTPWDKVMDADM--NEPRIEWFKGATLNVAYNC 96 Query: 82 LDRHLQENGDRT--AIIWEGDDASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAIYM 139 LDRHL NG R AIIW+G+ + ++Y+ L+ +VCRFA+ L LG++KGD VA+YM Sbjct: 97 LDRHLV-NGRRNKAAIIWQGEPEDDVRVLTYQMLYDEVCRFASVLQGLGVQKGDRVALYM 155 Query: 140 PMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIPLK 199 PM+PE AVAMLACARIGAVHS++F GFS ++ RI D +++V+T+D +RAGRSIPLK Sbjct: 156 PMIPELAVAMLACARIGAVHSIVFAGFSAVSLQNRIQDCEAKVVVTADAVLRAGRSIPLK 215 Query: 200 KNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHD-LVEQASDQH-QAEEMNAED 257 NVD+ALK+ SVE VVV+ R +EGRD+WWH+ + ++ D +M++ED Sbjct: 216 VNVDEALKD--CPSVERVVVVDRAHSNCAMREGRDMWWHEAMADRTLDTSCPCAKMDSED 273 Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317 LFILYTSGSTGKPKGV+HTTGGYL YAA T ++VFD H D+YWCTAD+GW+TGHSY++ Sbjct: 274 MLFILYTSGSTGKPKGVVHTTGGYLAYAAHTTQWVFDLHDDDVYWCTADIGWITGHSYIV 333 Query: 318 YGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377 YGPLA G TTLMFEGVP+WP P R +V+K +VNI YTAPT IRALM EG + D Sbjct: 334 YGPLALGGTTLMFEGVPSWPGPDRFWHIVEKFRVNIFYTAPTVIRALMREGAHWTQKHDL 393 Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSA 437 SSLR+LGSVGEPINPEAW WY + IG+ + P+VDTWWQTETGG MI+ LP AT LK GSA Sbjct: 394 SSLRVLGSVGEPINPEAWMWYHEHIGHSRLPIVDTWWQTETGGIMISALPYATTLKPGSA 453 Query: 438 TRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNMYF 497 T P G+ A+V +G P G LV+ WPG R +FG ER++ TYF F MY Sbjct: 454 TMPLPGIDAAVVKADGTPCGPNEGGHLVVRKPWPGMLRGVFGSPERYKSTYFERFPGMYE 513 Query: 498 SGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIKGQ 557 SGDGAR DEDGY W+ GR+DDV+NVSGHR+GTAE+ESALV+HP +AEAAVVG+PH IKG+ Sbjct: 514 SGDGARTDEDGYTWVMGRLDDVINVSGHRMGTAEVESALVSHPAVAEAAVVGMPHAIKGE 573 Query: 558 AIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILRK 617 AIYAYVTL+ G E + EL A +R WVRKEIGP+ATP+V+ + + LPKTRSGKIMRRILRK Sbjct: 574 AIYAYVTLSAGTEETEELRAALRTWVRKEIGPIATPEVIQFAEGLPKTRSGKIMRRILRK 633 Query: 618 IAAGDTSNLGDTSTLADPGVVEKLLE 643 IA+G S+ GDTSTLADPGVV+ L+E Sbjct: 634 IASGAGSDFGDTSTLADPGVVQDLIE 659 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: 1410 Number of extensions: 53 Number of successful extensions: 4 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: 667 Length adjustment: 38 Effective length of query: 614 Effective length of database: 629 Effective search space: 386206 Effective search space used: 386206 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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