Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate PP_4549 PP_4549 long-chain-fatty-acid/CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Putida:PP_4549 Length = 565 Score = 255 bits (651), Expect = 4e-72 Identities = 170/534 (31%), Positives = 267/534 (50%), Gaps = 30/534 (5%) Query: 54 GRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNIN 112 G+ TY +L + A+ L L PGDR+ + N ++ + + GL++VN N Sbjct: 47 GKTITYGELYALSGAFAAWLQQHTDLKPGDRIAVQLPNVLQYPVAVFGAMRAGLIVVNTN 106 Query: 113 PAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKL-PQLK 171 P Y E+E+ N G K LV +A + ++ P+ Q + + A L P LK Sbjct: 107 PLYTAREMEHQFNDSGAKALVCLANMAH-----LAEKVVPKTQVRHVIVTEVADLLPPLK 161 Query: 172 -----TVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSG 226 +V+ + + P +RF + +A G A QA D +Q+T G Sbjct: 162 RLLINSVIKYVKKMVPAYNLPQAVRFNDALALGKGQPV----TEANPQANDVAVLQYTGG 217 Query: 227 TTGFPKGATLTHRNILNNGFFIGECMKLTPADR------LCIPVPLYHCFGMVLGNLACF 280 TTG KGA LTHRN++ N +C L ++ L P+PLYH + +A Sbjct: 218 TTGVAKGAMLTHRNLVANML---QCRALMGSNLHEGCEILITPLPLYHIYAFTFHCMAMM 274 Query: 281 THGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMA 340 G V ++ D +++ + + +G G+ T+F+A ++ F + S L+ + Sbjct: 275 LIGNHNVLISNPRDLPAMVKELGKWKFSGFVGLNTLFVALCNNEAFRALDFSALKITLSG 334 Query: 341 GSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVK 400 G V +R + + I YGMTETSPV+ + ++ + +V T+G P K Sbjct: 335 GMALQLSVAERW-KAVTGCAICEGYGMTETSPVAAVNPSE---ANQVGTIGIPVPSTLCK 390 Query: 401 IVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYV 460 ++D D G +P+G+ GE C KG VM GYW E T E +D GW+ TGD+A + A+GY+ Sbjct: 391 VID-DAGNELPLGEVGELCVKGPQVMKGYWQREDATAEILDSEGWLKTGDIAVIQADGYM 449 Query: 461 NIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQ 520 IV R KDM++ G N+YP E+E+ L P V +GVPD+K GE + +I+ KPG Sbjct: 450 RIVDRKKDMILVSGFNVYPNELEDVLAALPGVLQCAAIGVPDEKSGEVIKVFIVVKPGMT 509 Query: 521 PTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKDQLGLEE 574 T++ + + + YKVPR+I F S P T GKI + ++RDE + GL++ Sbjct: 510 VTKEQVMEHMRANVTGYKVPRHIEFRDSLPTTNVGKILRRELRDEELKKQGLKK 563 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: 725 Number of extensions: 29 Number of successful extensions: 5 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: 565 Length adjustment: 36 Effective length of query: 542 Effective length of database: 529 Effective search space: 286718 Effective search space used: 286718 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