Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate RR42_RS36655 RR42_RS36655 hypothetical protein
Query= curated2:O53554 (515 letters) >FitnessBrowser__Cup4G11:RR42_RS36655 Length = 512 Score = 459 bits (1180), Expect = e-133 Identities = 258/516 (50%), Positives = 329/516 (63%), Gaps = 10/516 (1%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGA++L+ TL+ GVD CFANPGTSEMHFVAALD +P MR +L LFEGV TGAADGYAR Sbjct: 1 MNGAESLVKTLLACGVDTCFANPGTSEMHFVAALDRIPGMRCVLGLFEGVVTGAADGYAR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 +A +PAA LLH GPGL NGLANLHNARRA+ P++ +VGD ATYH+ +DAPL +D + A Sbjct: 61 MADKPAATLLHCGPGLANGLANLHNARRAQTPVINIVGDQATYHRPFDAPLTADTEGWAR 120 Query: 121 TVSGWVRRTEAAADVGADAEAAI-AASRSGSQIATLILPADVCWSDGAHAAAGVPAQ--- 176 VS W R AA VGADA A+ AA + +A+LILP+DVCW G GVP Sbjct: 121 PVSVWTRTATDAASVGADAATAVQAACAAPGGVASLILPSDVCWDAG--GKVGVPLAPLP 178 Query: 177 -AAAAPVDVGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLE 235 +P V A +LRSG+P ++++ G A R L A RI AT AR + + Sbjct: 179 VPKVSPDAVQQAARLLRSGQPTLIVLAGTALREVPLADAHRIAAATDARLITPMSNARVS 238 Query: 236 RGAGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLA 295 RG G V+R+ Y + A +L G+++++L GA PV+FFAYPG P E+HVLA Sbjct: 239 RGRGRFNVDRVPYSGDVARDKLAGIRNVILVGAPPPVTFFAYPGKSPRPYPEDAEIHVLA 298 Query: 296 EP-GGAADALAALADEVAPGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIVVDE 354 P A+ALA LADE+ +V+ A + + G +TS + A + ALLPE+AIVV+E Sbjct: 299 RPEQDLAEALARLADELGAPSVSVPASVAPRGIAKGAVTSEAVAQTLTALLPEQAIVVEE 358 Query: 355 SNTCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTI 414 S + G T A HDWL LTGGAIG G+P A GAAVAAP R V+ L++DGS MYT+ Sbjct: 359 SVSFGRAFYPGTVHAAPHDWLQLTGGAIGDGLPLATGAAVAAPGRRVVALQADGSGMYTL 418 Query: 415 SGLWSQARENLDVTTVIYNNGAYDILRIELQRVGAGSDPGPKALDLLDISRPTMDFVKIA 474 LW+ ARE LDVT VI N Y IL EL G G++PG ALD+LDI P +D+V++A Sbjct: 419 QSLWTMAREKLDVTVVILANRKYAILLGEL--AGVGANPGKTALDMLDIGNPDLDWVQLA 476 Query: 475 EGMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVV 510 GMGV A R E FA+ A GP +I++V+ Sbjct: 477 NGMGVEAARAEDMERFAELFGMANGRRGPFVIELVI 512 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: 640 Number of extensions: 24 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: 512 Length adjustment: 35 Effective length of query: 480 Effective length of database: 477 Effective search space: 228960 Effective search space used: 228960 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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