Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 352309 BT2782 long-chain-fatty-acid--CoA ligase (NCBI ptt file)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Btheta:352309 Length = 549 Score = 483 bits (1244), Expect = e-141 Identities = 241/540 (44%), Positives = 343/540 (63%), Gaps = 8/540 (1%) Query: 26 LIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVG 85 L E+T+G + P++E +V + R+T++QL +A L+ +G+ G VG Sbjct: 3 LFERTLGQWLEHWAEETPDKEYIVYSDRNLRFTWSQLNQRVDDMAKGLIAVGVERGTHVG 62 Query: 86 IWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLG 145 IW+ N +W+ + A A++G V V +N Y+ AE+EY L + K SD++ Sbjct: 63 IWAANVPDWLTLLYACAKIGAVYVTVNTNYKQAELEYLCQNSDMHTLCIVNGEKDSDFVQ 122 Query: 146 MLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGN-AADP 204 M + PE + + GHL++ + P +K V+++ E +G + E++ GN D Sbjct: 123 MTYTMLPELKTCERGHLKSERFPYMKNVIYVGQEKHRG-----MYNTAEILLLGNNVEDD 177 Query: 205 RLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPV 264 RL ++ + + D +N+Q+TSGTTGFPKG LTH NI NNGF GE MK T D+LC V Sbjct: 178 RLTELKSKVDCHDVVNMQYTSGTTGFPKGVMLTHYNIANNGFLTGEHMKFTADDKLCCCV 237 Query: 265 PLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHP 324 PL+HCFG+VL + C THG T V + FDPL VL ++ ERCT L+GVPTMFIAEL HP Sbjct: 238 PLFHCFGVVLATMNCLTHGCTQVMV-ERFDPLVVLASIHKERCTALYGVPTMFIAELHHP 296 Query: 325 RFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS 384 F F++S LRTGIMAGS CP E+MK+V E+M ++ +T YG+TE +P + D Sbjct: 297 MFDLFDMSCLRTGIMAGSLCPVELMKQVEEKMYMK-VTSVYGLTEAAPGMTATRIDDSFD 355 Query: 385 KRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGG 444 R +TVG+ EV+++DP+TG P+G +GE C +GY+ M GY+ + T E ID+ Sbjct: 356 VRCNTVGRDFEFTEVRVIDPETGEECPVGVQGEMCNRGYNTMKGYYKNPEATAEVIDKDN 415 Query: 445 WMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQK 504 ++H+GDL D +G I GRIKDM+IRGGENIYPREIEEFLY+ V+DVQV G+P +K Sbjct: 416 FLHSGDLGIKDEDGNYRITGRIKDMIIRGGENIYPREIEEFLYKLDGVKDVQVAGIPSKK 475 Query: 505 YGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 YGE + A+II + G + E D+R FCK +I+ YK+P+Y+ FV FPMT +GKIQKF+++D Sbjct: 476 YGEAVGAFIILQEGVEMHESDVRDFCKNKISRYKIPKYVFFVKEFPMTGSGKIQKFRLKD 535 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: 791 Number of extensions: 30 Number of successful extensions: 4 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: 578 Length of database: 549 Length adjustment: 36 Effective length of query: 542 Effective length of database: 513 Effective search space: 278046 Effective search space used: 278046 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: 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