Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF4204 HP15_4144 short chain acyl-CoA synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >FitnessBrowser__Marino:GFF4204 Length = 578 Score = 231 bits (589), Expect = 6e-65 Identities = 172/557 (30%), Positives = 273/557 (49%), Gaps = 50/557 (8%) Query: 28 EQTIGAFFADMVARQPEREALVSVH----QGRRYTYAQLQTEAHRLASALLGMGLTPGDR 83 ++ I +F VA P+REA+V TY +L + R+A+ L MG+ G+ Sbjct: 47 DKIITDYFDQAVASTPDREAIVGYQVTSDTRNALTYRELNDKVTRMAAGLAAMGIGKGEV 106 Query: 84 VGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDY 143 V N + + LA ++G +L + P +R E+ + L KLLV F+ DY Sbjct: 107 VACQLPNWWQTTALHLACMRIGAILNPLMPIFRERELRFMLKHGEAKLLVIPKVFRDFDY 166 Query: 144 LGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLR--------FTEL 195 M+ + E LP L+T++ I E G+ + E L+ T L Sbjct: 167 EAMVDGIRGE-------------LPALETLLVIGGE-GERSFEQRLMETPWEKQQDITSL 212 Query: 196 IARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLT 255 A L A D I I +TSGTTG PKG T + +N + + LT Sbjct: 213 FAERQ------------LTADDAIQILYTSGTTGEPKGVMHTSNTLFSNVRPYADRLHLT 260 Query: 256 PADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPT 315 D++ + PL H G + G + G T + D +D V + + E+ T Sbjct: 261 SDDKVLMASPLAHQTGFMYGIMMPVYLGTTAIL-QDIWDADYVCKVIGAEK-PAFTMAAT 318 Query: 316 MFIAEL--DHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPV 373 F+A+L P+ E L +LR + AG+P P+ V+++ + + + I A+GMTE V Sbjct: 319 PFLADLVKTAPKH-EGELDSLRIFVSAGAPIPSAVVEQAGKVLKAK-IVSAWGMTENGAV 376 Query: 374 SCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDE 433 + D P + + G+ P +EVK+ D G +P G+ G +G S+ GY + Sbjct: 377 TMTCPED-PAERASQSDGKAMPFMEVKVTDFQ-GNELPAGEEGSLLVRGSSLFVGYL--K 432 Query: 434 AKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQ 493 +DE GW +TGDLA MD + Y+ I GR KD+VIRGGENI E+E LY+ P + Sbjct: 433 RPELYGVDESGWFNTGDLARMDQDAYIRITGRTKDVVIRGGENIPVVEVENLLYKFPGIV 492 Query: 494 DVQVVGVPDQKYGEELCAWI-IAKPGTQPTEDDIRAF-CKGQIAHYKVPRYIRFVTSFPM 551 DV +VG PD++ GE LCA++ + + T T + ++ + + Q++ +P Y+ + + P Sbjct: 493 DVALVGCPDERLGERLCAYVTLDENATDLTLEQVKTYLTEQQLSKNYLPEYLEVIEAMPR 552 Query: 552 TVTGKIQKFKIRDEMKD 568 T +GKIQKFK+R++ ++ Sbjct: 553 TASGKIQKFKLREQARN 569 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: 682 Number of extensions: 33 Number of successful extensions: 7 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: 578 Length adjustment: 36 Effective length of query: 542 Effective length of database: 542 Effective search space: 293764 Effective search space used: 293764 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