Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate RR42_RS10650 RR42_RS10650 acetyl-CoA synthetase
Query= SwissProt::P39062 (572 letters) >FitnessBrowser__Cup4G11:RR42_RS10650 Length = 588 Score = 519 bits (1337), Expect = e-151 Identities = 272/571 (47%), Positives = 355/571 (62%), Gaps = 17/571 (2%) Query: 14 NLKNYEETYRHFDWAEAEKHFSWHETGKLNAAYEAIDRHAESFRKNKVALYYKDAKRDEK 73 NL +YE R F WA + + G LN A++A+DRHA S + K A Sbjct: 19 NLGDYEAERRVFSWAAVSRELADQPQGALNIAWQAVDRHAASSLRGKAAFRILARGTPTH 78 Query: 74 Y-TFKEMKEESNRAGNVLRRYGNVEKGDRVFIFMPRSPELYFIMLGAIKIGAIAGPLFEA 132 + T+ ++ +NR NVLR G V KG+R+FI R PELY +LG++K G PLF A Sbjct: 79 FVTYGQLSALTNRFCNVLRDLG-VGKGERLFILAGRIPELYIAILGSLKNGTAVSPLFSA 137 Query: 133 FMEGAVKDRLENSEAKVVVTTPELLERIPV---DKLPHLQHVFVV----GGEAESGTNII 185 F + R+ E V+VTT L ER D++P L+HV +V G A GT + Sbjct: 138 FGPDPIATRVNLGEGAVLVTTDMLFERKIAKWRDRMPSLKHVLLVAEDGGTTAVPGT--L 195 Query: 186 NYDEAAKQESTRLDIEWMDKKDGFLLHYTSGSTGTPKGVLHVHEAMIQQYQTGKWVLDLK 245 + S +I +D LLH+TSG+TGTPKG +HVH A++ + TG++ LDL Sbjct: 196 DLSSLMASASDACEITPTTAEDMALLHFTSGTTGTPKGAVHVHGAVLTHWSTGRYALDLH 255 Query: 246 EEDIYWCTADPGWVTGTVYGIFAPWLNGATNVIVGGRFSPESWYGTIEQLGVNVWYSAPT 305 +DIYWCTADPGWVTGT YG+ AP L+G T+++ F E WY ++ GV++WY+APT Sbjct: 256 VDDIYWCTADPGWVTGTSYGVIAPLLHGVTSIVDREEFDAERWYAILQDEGVSIWYTAPT 315 Query: 306 AFRMLMGAGDEMAAKYDLTSLRHVLSVGEPLNPEVIRWGHKVFNKRIHDTWWMTETGSQL 365 A RMLM AG ++A KY LR SVGEPLNPE + WG +V HD WW TETG + Sbjct: 316 AIRMLMKAGADIAKKYAFPRLRFAASVGEPLNPEAVWWGKQVLGLPFHDNWWQTETGGIM 375 Query: 366 ICNYPCMDIKPGSMGKPIPGVEAAIVDNQGNEL-----PPYRMGNLAIKKGWPSMMHTIW 420 I N P DIKPGSMG+P+PGVEAAIV Q + P + G LA+K+GWPSM Sbjct: 376 IANTPAFDIKPGSMGRPLPGVEAAIVSRQADGSVQVIEAPNKEGELALKRGWPSMFRGYL 435 Query: 421 NNPEKYESYFMPGGWYVSGDSAYMDEEGYFWFQGRVDDVIMTSGERVGPFEVESKLVEHP 480 N+ E+Y F G WY++GD A D +GY+WF GR DDVI ++G +GPFEVES L+EHP Sbjct: 436 NSEERYRKSF-SGEWYLTGDLARRDADGYYWFVGRADDVIKSAGHLIGPFEVESALMEHP 494 Query: 481 AIAEAGVIGKPDPVRGEIIKAFIALREGFEPSDKLKEEIRLFVKQGLAAHAAPREIEFKD 540 A+AEA VIGKPDP+ GE++KAF++L GFE S+ L+ + + L A AP+EI F Sbjct: 495 AVAEAAVIGKPDPIAGEVVKAFVSLNNGFEQSEALRMALLGHARTRLGAAVAPKEIAFLT 554 Query: 541 KLPKTRSGKIMRRVLKAWELNLPAGDLSTME 571 +LP+TRSGKIMRR+LKA EL LP GD ST+E Sbjct: 555 QLPRTRSGKIMRRLLKARELGLPEGDTSTLE 585 Lambda K H 0.318 0.136 0.425 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: 997 Number of extensions: 58 Number of successful extensions: 5 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: 572 Length of database: 588 Length adjustment: 36 Effective length of query: 536 Effective length of database: 552 Effective search space: 295872 Effective search space used: 295872 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: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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