Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf1N1B4_3988 Acetoacetyl-CoA synthetase (EC 6.2.1.16) / Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3988 Length = 568 Score = 621 bits (1602), Expect = 0.0 Identities = 310/561 (55%), Positives = 400/561 (71%), Gaps = 5/561 (0%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 S+ RG+ D L+ TIG F + VA+ P EALV HQ RYT+ QL A A L Sbjct: 11 SYTRGSQDKALLAMTIGQAFDNTVAQHPNGEALVVRHQQLRYTWQQLSETVDLHARAFLA 70 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 +GL GDR+GIW+ N A+W + Q A+A++G++LVNINPAYR++E+EY L + GC+ LV Sbjct: 71 LGLQTGDRLGIWAPNCAQWCISQFASAKIGVILVNINPAYRSSELEYVLKQSGCQWLVCA 130 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 +KTSDY GML+ L PE Q G LQ+ +LP+L+ V+ +D + G L T+L Sbjct: 131 GAYKTSDYHGMLQGLIPELAEQSIGQLQSERLPELRGVISLDAQPPSGFLPWSQL--TDL 188 Query: 196 IARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLT 255 A + + +L + L +NIQ+TSGTTGFPKGATL+H NILNNG+ +GE + LT Sbjct: 189 AA--SVSIEQLRERQDSLHFDQAVNIQYTSGTTGFPKGATLSHYNILNNGYMVGESLGLT 246 Query: 256 PADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPT 315 DRL IPVPLYHCFGMV+GNL C THG+T++YPND FDPL L TV +E+ T L+GVPT Sbjct: 247 ANDRLVIPVPLYHCFGMVMGNLGCVTHGSTMIYPNDAFDPLLTLSTVAEEKATALYGVPT 306 Query: 316 MFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSC 375 MFIA LD P+ AEF+LS+LRTGIMAG+ CP EVM+RV+ +M++ E+ IAYGMTETSPVS Sbjct: 307 MFIAMLDQPKRAEFDLSSLRTGIMAGATCPIEVMRRVINEMHMSEVQIAYGMTETSPVSL 366 Query: 376 QSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAK 435 Q+ L RV+TVG+ QP LE KI+D + G +VP G GE CT+GYSVM GYW + Sbjct: 367 QTGPSDELELRVTTVGRTQPQLESKIID-EAGNLVPRGTIGELCTRGYSVMLGYWNNPQG 425 Query: 436 TREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDV 495 T EAIDE GWMHTGDLA+M+ EGYV I GR KDM+IRGGENIYPRE+EEF + HP V DV Sbjct: 426 TAEAIDEAGWMHTGDLASMNDEGYVCIAGRNKDMIIRGGENIYPRELEEFFFTHPAVADV 485 Query: 496 QVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTG 555 QV+G+P +YGEE+ AWI PG TE +++A+CK +IAH+K PRY +FV FPMTVTG Sbjct: 486 QVIGIPCSRYGEEIVAWIKFHPGHSATEQELQAWCKERIAHFKTPRYFKFVEEFPMTVTG 545 Query: 556 KIQKFKIRDEMKDQLGLEEQK 576 KIQKF++R+ ++L +++ Sbjct: 546 KIQKFRMREISIEELASTDRQ 566 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: 907 Number of extensions: 33 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: 568 Length adjustment: 36 Effective length of query: 542 Effective length of database: 532 Effective search space: 288344 Effective search space used: 288344 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