Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate AZOBR_RS00270 AZOBR_RS00270 acetyl-CoA synthetase
Query= SwissProt::P27550 (652 letters) >FitnessBrowser__azobra:AZOBR_RS00270 Length = 646 Score = 919 bits (2374), Expect = 0.0 Identities = 430/637 (67%), Positives = 515/637 (80%), Gaps = 3/637 (0%) Query: 9 IPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIK 68 + IA ++ Y +Y+QSIN P+ FWGEQGK +DWIKPY KVK+ S+ G+V IK Sbjct: 9 VKQEIAKTAYVDEAAYARLYEQSINDPEAFWGEQGKRIDWIKPYSKVKDVSYT-GDVHIK 67 Query: 69 WYEDGTLNLAANCLDRHLQENGDRTAIIWEGDDASQSKHISYKELHRDVCRFANTLLELG 128 W+ DGTLN++ANC+DRHL GD+TAII+EGDD SKHI+YKELH VCR AN L + G Sbjct: 68 WFYDGTLNVSANCVDRHLATRGDQTAIIFEGDDPGVSKHITYKELHEQVCRLANVLKKNG 127 Query: 129 IKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDE 188 +KKGD V IY+PM+PEAA AMLACAR+GA+HS++FGGFSP+++ RI+D +S VITSDE Sbjct: 128 VKKGDRVTIYLPMIPEAAYAMLACARVGAIHSIVFGGFSPDSLKDRIVDCDSHFVITSDE 187 Query: 189 GVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQH 248 G+R GR +PLK N D A+ V+HV+V+K TGG + W EGRDLW+H+ + S Sbjct: 188 GLRGGRKVPLKANADKAVAA--APGVKHVLVVKHTGGNVAWTEGRDLWYHEEIASVSADC 245 Query: 249 QAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVG 308 EEM+AEDPLFILYTSGSTGKPKGVLHTTGGYLVYA++T +YVFDY G++YWCTADVG Sbjct: 246 PPEEMSAEDPLFILYTSGSTGKPKGVLHTTGGYLVYASMTHQYVFDYKDGEVYWCTADVG 305 Query: 309 WVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEG 368 WVTGHSY++YGPLA GATTLMFEGVP +P +R QVVDKH+VNI YTAPTAIR+LM EG Sbjct: 306 WVTGHSYIVYGPLANGATTLMFEGVPTYPDISRFWQVVDKHKVNIFYTAPTAIRSLMREG 365 Query: 369 DKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPG 428 + ++ T RSSLRILGSVGEPINPEAW WY+ +G+ +CP+VDTWWQTETGG +ITPLPG Sbjct: 366 EGPVKKTSRSSLRILGSVGEPINPEAWLWYYNVVGDGRCPIVDTWWQTETGGILITPLPG 425 Query: 429 ATELKAGSATRPFFGVQPALVDNEGNPLEGATEGSLVITDSWPGQARTLFGDHERFEQTY 488 A K GSAT+PFFGV+P +VDN+G LEG TEG+L I DSWPGQ RT+FGDHERF QTY Sbjct: 426 AIGQKPGSATKPFFGVKPVVVDNDGKELEGETEGNLCIADSWPGQMRTVFGDHERFVQTY 485 Query: 489 FSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVV 548 FSTF YF+GDG RRD DGYYWITGRVDDV+NVSGHR+GTAE+ESALVAHPK+AEAAVV Sbjct: 486 FSTFAGYYFTGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHPKVAEAAVV 545 Query: 549 GIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSG 608 G PH++KGQ IYAYVTLN GE P+ EL E+ WVRKEIGP+A+PD++ W+ LPKTRSG Sbjct: 546 GYPHDLKGQGIYAYVTLNAGESPTEELRKELVAWVRKEIGPIASPDLIQWSPGLPKTRSG 605 Query: 609 KIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645 KIMRRILRKIAA + +LGDTSTLADP VV L+E + Sbjct: 606 KIMRRILRKIAANEHDSLGDTSTLADPTVVTDLIENR 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: 1487 Number of extensions: 62 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 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