Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 202759 SO3664 long-chain-fatty-acid--CoA ligase (NCBI ptt file)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__MR1:202759 Length = 532 Score = 218 bits (556), Expect = 4e-61 Identities = 157/521 (30%), Positives = 253/521 (48%), Gaps = 36/521 (6%) Query: 54 GRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNIN 112 G+ ++ +++ ++ A+ L L PGDR+ I N ++V+ + GL+LVN N Sbjct: 38 GKNSSFNEIERDSRYFAAYLQNNTNLKPGDRIAIQLPNITQFVIAAYGALRAGLILVNTN 97 Query: 113 PAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKL--PQL 170 P Y E+ + N G K LV + SD L L ++ + L PQ+ Sbjct: 98 PLYTERELIHQFNDSGAKALVVL-----SDLLPTLAKVVATTPIELVISTHPLDLIDPQV 152 Query: 171 KTVVWIDD-EAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTG 229 + + + E + LL FT + P L+ +AA +Q+T GTTG Sbjct: 153 QPKTGLKNVEFCHVLQQGALLPFTRFV-------PTLSDLAA---------LQYTGGTTG 196 Query: 230 FPKGATLTHRNILNNGFFIGECMKLTPA---DRLCIPVPLYHCFGMVLGNLACFTHGATI 286 KGA LTH N+L N + + + D P+P+YH + ++ + F G Sbjct: 197 LSKGAMLTHGNMLANAAQVKSRIGSVISEGEDIFVAPLPIYHIYAFMVNLVLYFECGGCS 256 Query: 287 VYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPT 346 V + D +++T+ TG G+ T+F+A P F N S L+ I G+ T Sbjct: 257 VLIPNPRDINGLIKTLAKYPFTGFAGLNTLFVALCHQPEFKALNFSHLKITISGGTAL-T 315 Query: 347 EVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDT 406 + +Q I+ YG++ETSPV S + P +++ T+G+ EVK++D ++ Sbjct: 316 AAAANLWQQTTGNTISEGYGLSETSPVI---SLNAPGYQKIGTIGKPVLGTEVKLLD-ES 371 Query: 407 GAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRI 466 G V G GE +G VM GYW + +T + G+ TGD+A ++ EG+ IV R Sbjct: 372 GNEVTQGTAGELAARGPQVMLGYWNNPQETANVMTPDGFFKTGDIAILNEEGFHQIVDRK 431 Query: 467 KDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTE--- 523 KDM+I G N+YP E+E L HP + + VVGV D GE + A+I+ K +Q E Sbjct: 432 KDMIIVSGFNVYPNEVENVLASHPNIIECAVVGVKDDHSGEAVKAFIVLKDDSQDHEKIK 491 Query: 524 DDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564 I FC+ Q+ YK+P+ I F++ P + GKI + ++++ Sbjct: 492 TAILNFCREQLTAYKLPKQIEFMSQLPKSTVGKILRRELKN 532 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: 702 Number of extensions: 37 Number of successful extensions: 6 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: 532 Length adjustment: 36 Effective length of query: 542 Effective length of database: 496 Effective search space: 268832 Effective search space used: 268832 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