Align Putative acetolactate synthase large subunit IlvX; ALS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; AHAS (uncharacterized)
to candidate WP_012850499.1 TCUR_RS00525 acetolactate synthase large subunit
Query= curated2:O53554 (515 letters) >NCBI__GCF_000024385.1:WP_012850499.1 Length = 519 Score = 657 bits (1695), Expect = 0.0 Identities = 341/518 (65%), Positives = 400/518 (77%), Gaps = 5/518 (0%) Query: 1 MNGAQALINTLVDGGVDVCFANPGTSEMHFVAALDAVPRMRGMLTLFEGVATGAADGYAR 60 MNGAQAL++TLV+ V VCF+NPGTSEMH VAALD VPRMRG+L LFEGVATGAADGY R Sbjct: 1 MNGAQALLHTLVNADVQVCFSNPGTSEMHLVAALDTVPRMRGVLCLFEGVATGAADGYGR 60 Query: 61 IAGRPAAVLLHLGPGLGNGLANLHNARRARVPMVVVVGDHATYHKKYDAPLESDIDAVAG 120 +A PAAVLLHLGPGL NGLANLHNARRA P++ +VGDHATYH++YDAPLESDI A+AG Sbjct: 61 MASAPAAVLLHLGPGLANGLANLHNARRAGTPILNIVGDHATYHQRYDAPLESDIHALAG 120 Query: 121 TVSGWVRRTEAAADVGADAEAAIAASRS-GSQIATLILPADVCWSDGAHAAAGVPAQAAA 179 +VSGW+RR+ + DV ADA A+AA+ + Q+ATLILPADVCWS+GA A V ++ A+ Sbjct: 121 SVSGWIRRSARSRDVPADAAEAVAAALTPPGQVATLILPADVCWSEGAQPATPVRSRPAS 180 Query: 180 APVD--VGPVAGVLRSGEPAMMLIGGDATRGPGLTAAARIVQATGARWLCETFPTCLERG 237 D V A VL+SGEP +L+GG ATR GL AA RI ATGA+ LCETFP LERG Sbjct: 181 PVHDSVVESAAAVLKSGEPCALLLGGGATRRHGLEAAGRIAAATGAKLLCETFPARLERG 240 Query: 238 AGIPAVERLAYFAEGAAAQLDGVKHLVLAGARSPVSFFAYPGMPSDLVPAGCEVHVLAEP 297 AG+PAVERLAY E AAAQ+ G++HL+LAGA+ PVSFFAYP PSDLVP GC+VHVLA Sbjct: 241 AGLPAVERLAYLGEMAAAQMTGLRHLILAGAKRPVSFFAYPNQPSDLVPEGCQVHVLAGD 300 Query: 298 G-GAADALAALADEVAPGTVAPVAGASRPQLPTGDLTSVSAADVVGALLPERAIVVDESN 356 G AA ALA LAD VA G PV SRP+ P+G LT+ AA V+GALLPE AIV DESN Sbjct: 301 GDDAAGALAHLADLVAGGVAPPVQQPSRPEPPSGPLTAEKAAAVIGALLPEDAIVSDESN 360 Query: 357 TCGVLLPQATAGAPAHDWLTLTGGAIGYGIPAAVGAAVAAPDRPVLCLESDGSAMYTISG 416 T G+ L ATAGAP HDWLTLTGGAIG G+P A GAA+A P RPV+CLE+DGSAMYT+S Sbjct: 361 TSGLWLAGATAGAPPHDWLTLTGGAIGQGMPLATGAAIACPSRPVVCLEADGSAMYTLSA 420 Query: 417 LWSQARENLDVTTVIYNNGAYDILRIELQRVGAG-SDPGPKALDLLDISRPTMDFVKIAE 475 LW+QARE LDVTTVI+NNG+Y +L +EL RVGA + G A + D+SRP +DFV +A+ Sbjct: 421 LWTQAREGLDVTTVIFNNGSYAVLNMELARVGADPNSAGEAARSMFDLSRPDLDFVSLAQ 480 Query: 476 GMGVPARRVTTCEEFADALRAAFAEPGPHLIDVVVPSL 513 GMGVPA R T EE A A +EPGPHLI+ VVPS+ Sbjct: 481 GMGVPAGRARTAEELAAQFGKALSEPGPHLIEAVVPSV 518 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: 793 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: 519 Length adjustment: 35 Effective length of query: 480 Effective length of database: 484 Effective search space: 232320 Effective search space used: 232320 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 10 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