Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 15923 b1805 acyl-CoA synthase (NCBI)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Keio:15923 Length = 561 Score = 244 bits (622), Expect = 9e-69 Identities = 173/551 (31%), Positives = 269/551 (48%), Gaps = 25/551 (4%) Query: 29 QTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALL-GMGLTPGDRVGIW 87 Q++ F VAR ++ A V++ G T+ +L+ + A+ L G+GL GDRV + Sbjct: 23 QSLVDMFEQSVARYADQPAFVNM--GEVMTFRKLEERSRAFAAYLQQGLGLKKGDRVALM 80 Query: 88 SHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARF-----KTSD 142 N ++ + + G+++VN+NP Y E+E+ LN G +V ++ F K D Sbjct: 81 MPNLLQYPVALFGILRAGMIVVNVNPLYTPRELEHQLNDSGASAIVIVSNFAHTLEKVVD 140 Query: 143 YLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAA 202 + + Q L AK + VV P + F + G Sbjct: 141 KTAVQHVILTRMGDQ----LSTAKGTVVNFVVKYIKRLVPKYHLPDAISFRSALHNGY-- 194 Query: 203 DPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK--LTPADRL 260 R+ V L D +Q+T GTTG KGA LTHRN+L N + L P L Sbjct: 195 --RMQYVKPELVPEDLAFLQYTGGTTGVAKGAMLTHRNMLANLEQVNATYGPLLHPGKEL 252 Query: 261 CIP-VPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIA 319 + +PLYH F + + L G + + D +++ + T + GV T+F A Sbjct: 253 VVTALPLYHIFALTINCLLFIELGGQNLLITNPRDIPGLVKELAKYPFTAITGVNTLFNA 312 Query: 320 ELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSST 379 L++ F + + S+L G P V +R V+ + + + YG+TE +P+ + Sbjct: 313 LLNNKEFQQLDFSSLHLSAGGGMPVQQVVAERWVK-LTGQYLLEGYGLTECAPLVSVNPY 371 Query: 380 DTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREA 439 D + ++G P E K+VD D V P GQ GE C KG VM GYW T E Sbjct: 372 D--IDYHSGSIGLPVPSTEAKLVDDDDNEVPP-GQPGELCVKGPQVMLGYWQRPDATDEI 428 Query: 440 IDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVG 499 I + GW+HTGD+A MD EG++ IV R KDM++ G N+YP EIE+ + +HP VQ+V VG Sbjct: 429 I-KNGWLHTGDIAVMDEEGFLRIVDRKKDMILVSGFNVYPNEIEDVVMQHPGVQEVAAVG 487 Query: 500 VPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQK 559 VP GE + +++ K + TE+ + FC+ Q+ YKVP+ + F P + GKI + Sbjct: 488 VPSGSSGEAVKIFVVKKDPSL-TEESLVTFCRRQLTGYKVPKLVEFRDELPKSNVGKILR 546 Query: 560 FKIRDEMKDQL 570 ++RDE + ++ Sbjct: 547 RELRDEARGKV 557 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: 765 Number of extensions: 36 Number of successful extensions: 8 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: 561 Length adjustment: 36 Effective length of query: 542 Effective length of database: 525 Effective search space: 284550 Effective search space used: 284550 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