Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate BPHYT_RS31920 BPHYT_RS31920 acetate--CoA ligase
Query= BRENDA::D6EQU8 (658 letters) >FitnessBrowser__BFirm:BPHYT_RS31920 Length = 650 Score = 276 bits (705), Expect = 3e-78 Identities = 194/653 (29%), Positives = 304/653 (46%), Gaps = 36/653 (5%) Query: 6 PQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDV 65 P P+W P A ++ A++T A Y L+ +S+ +W + W + Sbjct: 5 PDPVWWPTATDVSNAQVTSLIR-------ALGLRDYDELYAYSIANPGEYWHRLMVWLGI 57 Query: 66 RFSTPYARVLG-DRTMPGAQWFPGATLNYAEHALR--AAGTRPDEPALLYVDETHEPAPV 122 R+ PY+ + P QWFPG LN+ + A R AL+ DE+ Sbjct: 58 RWQAPYSAYVDLSDGKPFPQWFPGGKLNWVDSIFECEADKERLQRIALIAEDESGRVTQR 117 Query: 123 TWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFGA 182 T+AELR V S AA L + PGD V + + ++VV LA + +G + FGA Sbjct: 118 TYAELREDVQSFAAGLMTSKLGPGDCVGLLMESSVESVVTYLALSYIGAIAVPLFSGFGA 177 Query: 183 RSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEAP-- 240 +++ R Q + L G+ GK RD + LP+L ++ P+ G++ Sbjct: 178 DAIVARLQGCDAKGLVATAGFMRRGKPVLTRDAIESSIPALPSLEVLVVKPMRGSQGSVH 237 Query: 241 DGTLDW-ETLTAADAEPVYEQVPFD--HPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQL 297 G LDW + L A AEP+ VP + P ++Y+SGTTG PK V + GG ++ Sbjct: 238 AGALDWYDVLAAGRAEPLDHAVPAEANTPCMIVYTSGTTGKPKGTVHTHGGFPLKIAHDA 297 Query: 298 GLHCDLGPGDRFFWYTSTGWMMWNFLVSG-LLTGTTIVLYDGSPGFPATDAQWRIAERTG 356 ++ +LG GDR+ W GW+ ++G L G T+V YDG+P P ++ R Sbjct: 298 AVYFNLGAGDRWLWPADMGWVAGPITIAGAFLRGATLVCYDGAPNCPDWSRLPQLIRRYA 357 Query: 357 ATLFGTSAAYV--MACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGAD 414 T FG S + ++ ++ + P DLS+++ T G + + FRW + FA Sbjct: 358 VTHFGASPTLIRTLSAHESSIAPD---DLSSVRLAITAGEVIDSESFRWYGERFACP--- 411 Query: 415 LWIASVSGGTDVCSCFAGAVPTLPVHIGELQ--APGLGTDLQSWDPSGDPLTDEVGELVV 472 + + +GG++V G V P+ G APG+ D++ D G + EVGEL V Sbjct: 412 --VINFTGGSEVSGGLLGNVVVKPIVPGGFNAIAPGIRVDVRGAD--GKQVRGEVGELAV 467 Query: 473 TNPMPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQG 532 P M FW +P+ RY D+Y+ P VW HGD + V+ GRSD TL G Sbjct: 468 LEPFVGMTRSFWKNPE--RYLDTYWRNVPDVWIHGDLAIQFDDHAFVLCGRSDDTLKIAG 525 Query: 533 VRMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIR 592 R+G ++I + + + E+ E+ +GI P G + +FV +A A ++I + Sbjct: 526 KRVGPSEIEDVIVEIAEVAEAAAVGISDPVKGQRLVVFV-VADKERCTVAFREQIVDMVS 584 Query: 593 VNLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAV---NPGSID 642 L P +V V +P T +GK + +KR +G PL NP +I+ Sbjct: 585 RRLGKPFAPSQVYVVGELPKTRSGKIMRRLIKRAYEGQPLGDTASLENPWAIE 637 Lambda K H 0.320 0.138 0.442 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: 1250 Number of extensions: 81 Number of successful extensions: 10 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: 658 Length of database: 650 Length adjustment: 38 Effective length of query: 620 Effective length of database: 612 Effective search space: 379440 Effective search space used: 379440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 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