Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases
Query= reanno::Marino:GFF2751 (415 letters) >FitnessBrowser__Cola:Echvi_1071 Length = 391 Score = 280 bits (717), Expect = 4e-80 Identities = 171/411 (41%), Positives = 237/411 (57%), Gaps = 34/411 (8%) Query: 9 DAYIVDAIRTPIGRYG-GALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAG 67 DAYI+ RT +G+ G R DDL IK L P L+ ++DD++ G A Sbjct: 2 DAYIIKGYRTAVGKAKKGGFRFYRPDDLAVDVIKKLIADTPGLEAERVDDLIVGNAVPEA 61 Query: 68 EDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMS 127 E + RM L+A L VPG INR CGSG++A+ A I++G +IAGG ESMS Sbjct: 62 EQGMQMGRMISLMA-LGKVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMS 120 Query: 128 RAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISREDQ 187 P +MG + T + W+ + Y + SM TAE +A D+ ISRED Sbjct: 121 MVP-MMG------------YKTALNWKIASE--HPDYYL-SMGLTAEELAKDYDISREDS 164 Query: 188 DAFALRSQQRTAAAQKEGRLAAEITPVTIP--------RRKQDPLVVDTDEHPRE-TSLE 238 D FA+ S +R +A KEGR EI P+ + +R+ VDTDE PR T+++ Sbjct: 165 DQFAVTSHERAISAIKEGRFKEEIVPIEVEETFVDASGKRQTRTFTVDTDEGPRPGTNMD 224 Query: 239 KLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEPR 298 L L F++ G VTAGN+S +DGA ++ +K+ NL+P AR+V+ + AGV+PR Sbjct: 225 VLGGLKPAFKQGGQVTAGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPR 284 Query: 299 IMGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGAI 358 IMG GP A K L AG++++D+ ++ELNEAFAAQALAV R L + D VN NGGA+ Sbjct: 285 IMGIGPKEAVPKALKQAGMKMSDISLVELNEAFAAQALAVIRALDM--DPNTVNVNGGAV 342 Query: 359 ALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIE 409 ALGHPLG +GA+L +NEL RR+ +Y + T C+G GQG+A ++E Sbjct: 343 ALGHPLGCTGAKLTVQMINELRRRN-----QKYGMVTACVGGGQGVAGVVE 388 Lambda K H 0.318 0.133 0.382 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: 410 Number of extensions: 20 Number of successful extensions: 7 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: 415 Length of database: 391 Length adjustment: 31 Effective length of query: 384 Effective length of database: 360 Effective search space: 138240 Effective search space used: 138240 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: 50 (23.9 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