Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate SMa0150 SMa0150 malonyl-CoA synthase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Smeli:SMa0150 Length = 508 Score = 230 bits (587), Expect = 9e-65 Identities = 167/527 (31%), Positives = 256/527 (48%), Gaps = 45/527 (8%) Query: 40 ARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQL 99 A +P+ A + GR +TY + + R+AS L +G+ PGDRV + + E +++ L Sbjct: 12 AARPD-SAFILTADGRVWTYGDMLEHSGRIASVLDALGVRPGDRVAVQVEKSPEALMLYL 70 Query: 100 ATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQP 159 A + G V + +N AY AE++Y +L+V K G+ + A Sbjct: 71 ACLRTGAVYLPLNTAYTLAELDYFFGDAEPRLIVCAPGAKE----GIAKHAAD------- 119 Query: 160 GHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPI 219 A++ L DE G G+ L+ +ARG A D A D Sbjct: 120 ---CGAEVETL-------DEKGGGS----LID----LARGKAPD----FPDADRGPDDLA 157 Query: 220 NIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLAC 279 I +TSGTTG KGA LTH N+L+N + E + T DRL +P++H G+ + + Sbjct: 158 AILYTSGTTGRSKGAMLTHDNLLSNATTLREYWRFTADDRLIHALPIFHTHGLFVASNVI 217 Query: 280 FTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIM 339 GA++ + FD VL+ + T + GVPT ++ + +P + +R + Sbjct: 218 LLAGASMFFLPK-FDANEVLRLMPQS--TSMMGVPTFYVRLVQNPGLTHEATAGMRLFVS 274 Query: 340 AGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS--KRVSTVGQVQPHL 397 +P E R QM I YGMTET+ +T P + TVG P + Sbjct: 275 GSAPLLAET-HRTFAQMTGHAILERYGMTETN-----MNTSNPYDGERIAGTVGFPLPGV 328 Query: 398 EVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAE 457 +++ DP++G +P G+ G KG +V GYW KT+ G+ TGDL +D Sbjct: 329 SLRVADPESGRPLPKGETGMIEVKGPNVFKGYWRMPEKTQGEFRADGFFITGDLGRIDER 388 Query: 458 GYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP 517 GYV+IVGR KD+VI GG NIYP+E+E + + P V + V+G+P +GE + A ++ KP Sbjct: 389 GYVHIVGRGKDLVISGGYNIYPKEVETEIDQMPGVVETAVIGLPHPDFGEGVTAVVVRKP 448 Query: 518 GTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 G E I +G++A YK P+ + FV P GK+QK +R+ Sbjct: 449 GAAIDERAILDGLEGRLARYKQPKRVIFVDDLPRNTMGKVQKNVLRE 495 Lambda K H 0.320 0.136 0.412 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: 678 Number of extensions: 34 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 508 Length adjustment: 35 Effective length of query: 543 Effective length of database: 473 Effective search space: 256839 Effective search space used: 256839 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: 52 (24.6 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