Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate PP_4063 PP_4063 putative Long-chain-fatty-acid-CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Putida:PP_4063 Length = 560 Score = 620 bits (1599), Expect = 0.0 Identities = 310/551 (56%), Positives = 389/551 (70%), Gaps = 9/551 (1%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 S+ RG D PL+ QTIG F VAR + EALVS HQG RY++ QL + A AL+ Sbjct: 5 SYTRGRQDRPLLTQTIGQAFDATVARCCDSEALVSRHQGLRYSWRQLAEQVEIYARALIA 64 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 +G+ GDRVGIWS N A+W ++QLA+A+VG +LVNINPAYR E+EY L + GC+ LV Sbjct: 65 LGVNTGDRVGIWSPNCAQWCILQLASAKVGAILVNINPAYRVGELEYVLRQSGCRWLVCA 124 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEP-GLLRFTE 194 FKTSDY M++EL PE PG L + LP+L+ V+ + A+ P G L + Sbjct: 125 EAFKTSDYHTMVQELVPELASAAPGELASECLPELRGVISL------AANPPAGFLPWHA 178 Query: 195 LIAR-GNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMK 253 R G + LQ P+NIQ+TSGTTG PKGATL+H NILNNGF +GE + Sbjct: 179 FAERAGQTSVEACTARQQSLQFDQPVNIQYTSGTTGAPKGATLSHYNILNNGFMVGESLG 238 Query: 254 LTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGV 313 LT DR+ IPVPLYHCFGMV+ NL C THG+T++YPND FD L+ V +ER T L+GV Sbjct: 239 LTARDRMVIPVPLYHCFGMVMANLGCITHGSTMIYPNDAFDAELTLRAVAEERATILYGV 298 Query: 314 PTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPV 373 PTMFIA LDHP A +LSTLR+GIMAG+ CP EVM+RV++QM++ E+ IAYGMTETSPV Sbjct: 299 PTMFIAMLDHPSRAHMDLSTLRSGIMAGATCPIEVMRRVIDQMHMAEVQIAYGMTETSPV 358 Query: 374 SCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDE 433 S Q+ D L RV+TVG+ QP LE K+VD D G +VP G+ GE CT+GYSVM GYW + Sbjct: 359 SLQTGPDDDLELRVTTVGRTQPQLENKLVDAD-GCIVPRGEIGELCTRGYSVMLGYWDNP 417 Query: 434 AKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQ 493 T +AID GWMH+GDLA MD +GYV IVGR KDM+IRGGENIYPRE+EEF Y HP V Sbjct: 418 QATADAIDPAGWMHSGDLAVMDEQGYVRIVGRNKDMIIRGGENIYPRELEEFFYTHPAVA 477 Query: 494 DVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTV 553 D QV+G+P +YGEE+ AWI PG T ++++ +CK +IAH+KVPRYIRFV +PMTV Sbjct: 478 DAQVIGIPCSRYGEEIVAWIKLHPGHSATVEELQGWCKARIAHFKVPRYIRFVDEYPMTV 537 Query: 554 TGKIQKFKIRD 564 TGK+QKF++R+ Sbjct: 538 TGKVQKFRMRE 548 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: 877 Number of extensions: 23 Number of successful extensions: 3 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: 560 Length adjustment: 36 Effective length of query: 542 Effective length of database: 524 Effective search space: 284008 Effective search space used: 284008 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