Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_025274859.1 HALAL_RS0115420 AMP-dependent synthetase
Query= reanno::acidovorax_3H11:Ac3H11_3009 (578 letters) >NCBI__GCF_000527155.1:WP_025274859.1 Length = 525 Score = 154 bits (389), Expect = 8e-42 Identities = 108/357 (30%), Positives = 179/357 (50%), Gaps = 12/357 (3%) Query: 216 TDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPV-PLYHCFGMVL 274 +D I F+ GTTG K THR ++++ + + +PV P +H +G + Sbjct: 169 SDRALIMFSGGTTGGSKSIPHTHRAMMDSVRRMEWGWPTPARGDVWLPVAPFFHIYGFLH 228 Query: 275 GNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHG-VPTMFIAELDHPRFAEFNLST 333 G A+IV P + F P V+ + R T G P ++ A L F +LST Sbjct: 229 GVANPVFGRASIVVP-ERFQPDHVVDLMGKHRVTVFGGGPPAIYNALLSAENFDSTDLST 287 Query: 334 LRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQV 393 LR+ G+P P E+++R E+ + +I YGMTE +P++ ++T + TVG Sbjct: 288 LRSCPAGGAPFPVELLRRWKERSGI-DIFEGYGMTEIAPLTVNTAT---FGAKAGTVGTA 343 Query: 394 QPHLEVKIVD-PDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLA 452 P ++V+I + V+ GQ+GE KG + Y T A +G +++TGD+ Sbjct: 344 APDVDVEITEIGHRDRVLAPGQKGEIRVKGPHLFAAYLNRPDDTAAAFTDG-YLYTGDVG 402 Query: 453 TMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAW 512 +D +G++ I R+KD++ G N++PRE+EE L HP V V VVG+P + E++ A+ Sbjct: 403 HLDEDGFLTISDRLKDVIFVKGFNVFPREVEEVLTNHPAVDAVGVVGIPHDRTDEQVIAF 462 Query: 513 IIAKPG-TQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRDEMKD 568 + PG +P + ++ C + YK P +I V P+T K+ + +R D Sbjct: 463 V--TPGDAEPDVERLQQHCAEHLVAYKQPAHIHLVDRLPLTGARKLDRMALRRSALD 517 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: 728 Number of extensions: 45 Number of successful extensions: 5 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: 525 Length adjustment: 36 Effective length of query: 542 Effective length of database: 489 Effective search space: 265038 Effective search space used: 265038 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 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