Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_012566670.1 RC1_RS07065 acetolactate synthase isozyme II large subunit
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000016185.1:WP_012566670.1 Length = 585 Score = 247 bits (631), Expect = 9e-70 Identities = 181/555 (32%), Positives = 264/555 (47%), Gaps = 32/555 (5%) Query: 17 APQTISGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTH 76 +P SG L+DAL HG D F G + L + DA A ++ I R E Sbjct: 29 SPPPRSGGRLLVDALVGHGADMAFCVAGESYLEVLDA---AVDRPELRLITCRQEGGAAF 85 Query: 77 AADAYARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQET 136 A+AY + TG+ G+C T GPGA N G+ + DS P++++ GQV R +AFQE Sbjct: 86 MAEAYGKLTGRPGICMVTRGPGACNAAIGVHASMQDSTPLILLVGQVARDQADREAFQEI 145 Query: 137 DIFGITLPIVKHSWVVR-DPAD-LGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQFNYVP 194 D + P+ K W + D AD + +A+AF A SGRPGPV++ +P+D+ +E Sbjct: 146 DYRRMFGPVAK--WAAQIDRADRIPEYLARAFRTATSGRPGPVVLALPEDMLRESAAVAD 203 Query: 195 VEPGSVIPGGFHQPEPPLDAAVAAALDLIEQAQRPLLYVGGGAISACAHDSLRMLAERYQ 254 + P + QP P AA+ L+ QA++PL+ VGG A LR AE + Sbjct: 204 LPPALPV-----QPHPD-PAALERMTALLAQARQPLMLVGGSGWDDPACARLRAFAEAWD 257 Query: 255 LPVTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVTGKLDTF 314 LPV + + + + VG LG + DLL+AVG R + T Sbjct: 258 LPVACSFRRQDVMANDSSCYVGDLGTGPNPALVERLRRADLLLAVGTRLGEIPTQGYTLP 317 Query: 315 AP---RARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERI 371 AP A ++H DP E+G+ + D+AVL G + +L A + W E Sbjct: 318 APPRAAATLIHVHPDPEELGRVYQPDLAVLA--GTAAFAAAAAALPAPAVRPWSGWREAA 375 Query: 372 N----TWKDRYPLTIPPAEGA-IYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQHLRNG 425 W++ PPA G + V +R+ P DA+VT D G W + LR G Sbjct: 376 RAEFLAWQE------PPAYGGDLDLGRVFGWLRERLPADAVVTNDAGNFSGWGHRFLRYG 429 Query: 426 PRGWISSAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKV 485 G G MG+G+PAA+ A + P+R VC+ GD M QEL T +G + Sbjct: 430 RPGRQLGPTCGAMGYGVPAAVAASLLRPERPAVCLVGDGGFTMTGQELATALHHGATPLI 489 Query: 486 VIVNNHWQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLA 545 ++ NN G +R QE+ + R SA+D+ N PDF ALAR++G G ++ E Sbjct: 490 LVFNNGMYGTIRMHQETRFPGRVSATDLTN--PDFAALARAYGAFGAAVSRTEEFAPAFE 547 Query: 546 AALQSPTPTMIDVHV 560 AAL S +I++ + Sbjct: 548 AALASGRAAVIELRM 562 Lambda K H 0.320 0.136 0.414 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: 1033 Number of extensions: 49 Number of successful extensions: 6 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: 617 Length of database: 585 Length adjustment: 37 Effective length of query: 580 Effective length of database: 548 Effective search space: 317840 Effective search space used: 317840 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 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