Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate AZOBR_RS23050 AZOBR_RS23050 decarboxylase
Query= BRENDA::O53554 (515 letters) >FitnessBrowser__azobra:AZOBR_RS23050 Length = 515 Score = 476 bits (1226), Expect = e-139 Identities = 270/516 (52%), Positives = 330/516 (63%), Gaps = 11/516 (2%) Query: 3 GAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYARIA 62 GA+ L+ TLV GVD CFANPGTSE+H +AA D++P R + TLFEGVATGAADGYAR+ Sbjct: 3 GAEILVRTLVANGVDTCFANPGTSELHALAAFDSMPGARCVPTLFEGVATGAADGYARMT 62 Query: 63 GRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAGTV 122 RPAA LLHLGPGL NGLANLHNARRA VPMV +VGDHAT+H+ DAPL SD++ +A + Sbjct: 63 DRPAATLLHLGPGLANGLANLHNARRACVPMVNIVGDHATWHRGVDAPLTSDVEGLAKPM 122 Query: 123 SGWVRRTEAAADVGAD-AEAAIAASRSGSQIATLILPADVCWSDGAHAAAGV---PAQAA 178 S WVR AA V AD AEA AA ++TLILP+D W D A A + PA AA Sbjct: 123 SAWVRTVPDAASVAADTAEAIRAALTPPCGVSTLILPSDSSWDDTAAAEPIIVEPPAPAA 182 Query: 179 AAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERGA 238 + A LRSGE ++L+ G ATR GL A RI ATGA+ T T +ERGA Sbjct: 183 PDADALRAAADALRSGERVVVLLNGRATRTEGLALAGRIAAATGAKLYAHTGATRIERGA 242 Query: 239 GIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEPG 298 G VER Y + A L G KH+VL G+ PV FF YP PS L P C +H +A PG Sbjct: 243 GRVTVERFPYPIDLGIAALAGAKHVVLIGSGEPVGFFGYPDKPSRLAPEDCRIHTVAPPG 302 Query: 299 GAADALAA---LADEV-APGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIVVDE 354 ADALAA LA+ V GT P + P+ TG LT+ S + ALLPE AIVVDE Sbjct: 303 --ADALAALRWLAEAVGCAGTPVPAQPLAPPEPATGALTADSVGQSLAALLPEGAIVVDE 360 Query: 355 SNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTI 414 + ++ A AGA AHDWLT+TGGAIG G+P A+GAA+A PDR V+ +++DGS MYT+ Sbjct: 361 GISSSPMVYTACAGARAHDWLTITGGAIGIGMPLALGAAIACPDRKVVTVQADGSGMYTL 420 Query: 415 SGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIA 474 LWSQARE DV T+I+ N Y IL+ EL +G D GP A + ++ RP +D+V +A Sbjct: 421 QALWSQARERADVVTIIFANRRYGILQWELGNLGF-RDMGPNARNCTELGRPDLDWVALA 479 Query: 475 EGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 GMGV + T E F L AAFA GP LI+ V+ Sbjct: 480 RGMGVEGGQATDAESFNRLLTAAFARKGPFLIEAVI 515 Lambda K H 0.318 0.134 0.402 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: 665 Number of extensions: 32 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: 515 Length of database: 515 Length adjustment: 35 Effective length of query: 480 Effective length of database: 480 Effective search space: 230400 Effective search space used: 230400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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