Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_024888968.1 Z164_RS0101410 AMP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000559025.1:WP_024888968.1 Length = 507 Score = 150 bits (378), Expect = 2e-40 Identities = 149/545 (27%), Positives = 231/545 (42%), Gaps = 63/545 (11%) Query: 31 IGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHN 90 +G F V R PE AL V R YA + + L G+ GD V N Sbjct: 4 LGTTFLAAVERDPE--ALAIVDGDVRLDYAAWYHAISSVVAGLEAAGVKRGDHVVSVLRN 61 Query: 91 NAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLREL 150 E + A G +LV +N +V + ++ + +V Sbjct: 62 RWEAATLHWACQFAGAILVPLNWRATAEDVAFCVHDSEARAIV----------------- 104 Query: 151 APEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVA 210 ++ + AA L V +D D G RF + +A D AQ Sbjct: 105 ---YEDAPAKAIAAAGLDDAVLHVTLD------VDRAGAQRFGDWLA----VDAPPAQPL 151 Query: 211 AGLQATDPINIQFTSGTTGFPKGATLTHR--------NILNNGFFIGECMKLTPADRLCI 262 A A D + +TSGTT PKG HR +I N + G R Sbjct: 152 A--VAEDWSLMLYTSGTTSKPKGVPRRHRAERAAAIAHIAQNRYRNGA--------RTLG 201 Query: 263 PVPLYHCFGMVLGNLAC-FTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAEL 321 +PLYH G V LAC +G + P FD L+ + ER L+ VPT++ L Sbjct: 202 VMPLYHTMG-VRSLLACALLNGTFVCLPK--FDAGQALRLIAAERIDNLYLVPTLYHDLL 258 Query: 322 DHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDT 381 HP FA ++ ++RT AG+ +++++ YG +E + + + Sbjct: 259 QHPDFAATDIGSVRTLGFAGASMTDGLLQKLQAAFAPELFVNHYGSSEIYTFTIEDDAPS 318 Query: 382 -PLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCT--KGYSVMHGYWGDEAKTRE 438 P S S + Q+ + + D T A + G+ G GYW + Sbjct: 319 KPGSAGRSGLNQMVRVVPLDATDAHTRAAP--NEEGQIVALLAGDEAFEGYWRRPDADAK 376 Query: 439 AIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVV 498 A+ GGW TGD +D +G + + GR+ DM+I GGEN+ P EIE L HP+V +V VV Sbjct: 377 AL-RGGWYFTGDTGYVDEDGDLFVTGRVDDMIISGGENVSPVEIESHLSLHPRVGEVAVV 435 Query: 499 GVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCK-GQIAHYKVPRYIRFVTSFPMTVTGKI 557 G+PD+++G + A++ + TED++ A+C+ ++A++K PR FV P + GK+ Sbjct: 436 GLPDERWGSVVTAFV--RRNGPVTEDELDAWCRDSKLANFKRPRRFVFVEDIPKSPVGKL 493 Query: 558 QKFKI 562 + K+ Sbjct: 494 LRRKL 498 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: 636 Number of extensions: 32 Number of successful extensions: 4 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: 507 Length adjustment: 35 Effective length of query: 543 Effective length of database: 472 Effective search space: 256296 Effective search space used: 256296 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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