Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate PP_3458 PP_3458 Butyrate--CoA ligase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Putida:PP_3458 Length = 562 Score = 625 bits (1611), Expect = 0.0 Identities = 309/556 (55%), Positives = 395/556 (71%), Gaps = 7/556 (1%) Query: 16 SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75 S+ +G D PL+ Q IG F VAR P+REALV HQ RYT+ QL + A AL+ Sbjct: 5 SYTQGTQDKPLLTQCIGDAFDATVARFPDREALVVHHQALRYTWRQLADAVDQHARALMA 64 Query: 76 MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135 +G+ PGDR+GIW+ N AEW + Q A+A+VG +LVNINPAYR++E++YAL + GC+ ++ Sbjct: 65 LGVQPGDRLGIWAPNCAEWCITQFASAKVGAILVNINPAYRSSELDYALGQSGCRWVICA 124 Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195 FKTSDY ML+ L P QPG L + P+L+ VV + + PG L + L Sbjct: 125 DAFKTSDYHAMLQGLLPGLASSQPGALICERFPELRGVVSL-----ALSPPPGFLAWHAL 179 Query: 196 IARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254 AR LA A L+ DPINIQ+TSGTTGFPKGATL+H NILNNG+ +GE + L Sbjct: 180 QARAEVVSGEALAARQAQLRCDDPINIQYTSGTTGFPKGATLSHSNILNNGYMVGESLGL 239 Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314 T DRL +PVPLYHCFGMV+ NL C THG+ ++YP+D FDPL L+ V E+ T L+GVP Sbjct: 240 TEHDRLVVPVPLYHCFGMVMANLGCMTHGSALIYPSDAFDPLATLRAVAQEKATALYGVP 299 Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374 TMFIAELDHP+ EF+LS+LRTGIMAG+ CP EVM+RV+ +M++ E+ IAYGMTETSPVS Sbjct: 300 TMFIAELDHPQRGEFDLSSLRTGIMAGATCPIEVMRRVIGEMHMAEVQIAYGMTETSPVS 359 Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434 Q+ L +RV++VG+ QP LE K+VD + G VP G+ GE CT+GYSVM GYW + Sbjct: 360 LQTGAADDLERRVTSVGRTQPRLESKVVDAE-GNTVPRGEIGELCTRGYSVMLGYWNNPK 418 Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494 T E+ID GWMHTGDLA MD +GYV IVGR KDM+IRGGENIYPRE+EEF + HP V D Sbjct: 419 ATAESIDAEGWMHTGDLAVMDEQGYVRIVGRSKDMIIRGGENIYPRELEEFFFTHPAVAD 478 Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554 VQV+GVP KYGEE+ AW+ PG +E ++R + + +IAH+KVPRY RFV FPMTVT Sbjct: 479 VQVIGVPCSKYGEEIVAWVRLHPGHAVSEVELREWARARIAHFKVPRYFRFVDEFPMTVT 538 Query: 555 GKIQKFKIRDEMKDQL 570 GK+QKF++R+ ++L Sbjct: 539 GKVQKFRMREISVEEL 554 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: 884 Number of extensions: 32 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: 562 Length adjustment: 36 Effective length of query: 542 Effective length of database: 526 Effective search space: 285092 Effective search space used: 285092 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