Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate YP_425376.1 Rru_A0284 thiamine pyrophosphate protein
Query= curated2:Q7U5G1 (617 letters) >NCBI__GCF_000013085.1:YP_425376.1 Length = 576 Score = 259 bits (662), Expect = 2e-73 Identities = 179/548 (32%), Positives = 265/548 (48%), Gaps = 32/548 (5%) Query: 22 SGAAALMDALRRHGVDTIFGYPGGAILPIYDALHIAESEGWVKHILVRHEQAGTHAADAY 81 +G A L D+L G DT++ PG + LP DA+H + ++ ++ R E ++ ADA+ Sbjct: 27 TGGALLADSLIALGADTVYCVPGESFLPFLDAVH--DRTDALRLVVCRQEGGASYMADAH 84 Query: 82 ARATGKVGVCFGTSGPGATNLVTGIATAQMDSVPMVVITGQVPRPAIGTDAFQETDIFGI 141 A+ TGK GVCF T GPGA N G+ TA D PM++ GQV RP IG +AFQE D+ Sbjct: 85 AKMTGKPGVCFVTRGPGACNAAIGVHTAFQDCTPMLLFIGQVDRPMIGREAFQEVDMTAF 144 Query: 142 TLPIVKHSWVVRDPADLGSIVAQAFLIAASGRPGPVLIDIPKDVGQEQ-FNYVPVEPGSV 200 P+ K S A L +VA+A+ A SGRPGP ++ +P+DV E F P+ Sbjct: 145 FAPLAKFSATADSAARLPELVARAWAAATSGRPGPAVVALPEDVLAEMAFARDPL----- 199 Query: 201 IPGGFHQPEPPLDAAVAAA--LDL---IEQAQRPLLYVGGGAISACAHDSLRMLAERYQL 255 P PP A AA DL + A+RPL+ VGGG + A + AE L Sbjct: 200 -------PRPPARPAPRAADMADLASRLAAAERPLVIVGGGTWTPRAAKLVTTWAEASGL 252 Query: 256 PVTTTLMGKGAFDENDALSVGMLGMHGTAYANFAVTECDLLIAVGARFDDRVT---GKLD 312 PV + D + +G LG + N + DL++ VG R + T ++ Sbjct: 253 PVVAAFRRQDVVDNLSPVYIGELGFSASPRLNARIKAADLIVCVGDRLGEVTTQGYSLIE 312 Query: 313 TFAPRARVVHFEIDPAEIGKNRKADVAVLGDLGLSLARMVEISLQRTAEPRTAAWLERIN 372 + P ++H D EIG+ D+ ++ + A M L A WL + Sbjct: 313 SPVPSQSLIHIFPDAGEIGRVYATDLGIVSAME-PFAEM----LSPVDGRHWAGWLAQ-G 366 Query: 373 TWKDRYPLTIPPAEGAIYPQEVLLAVRDLAP-DAIVTTDVGQHQMWAAQHLRNGPRGWIS 431 L P G++ +V+ + P DA++T G + W + R Sbjct: 367 RADYAANLRADPCPGSVDMAQVMAEIEARLPEDAVITNGAGNYSGWVHRFHRYRHFPSQL 426 Query: 432 SAGLGTMGFGMPAAMGAQVAMPDRQVVCIAGDASILMNIQELGTLAAYGLPVKVVIVNNH 491 + G G+MG+G+PAA+ A+V P R VV AGD LMN QEL T GL ++++NN Sbjct: 427 APGNGSMGYGLPAAIAAKVVAPRRVVVAFAGDGCFLMNGQELATAVDQGLDPIIIVINNG 486 Query: 492 WQGMVRQWQESFYDERYSASDMLNGMPDFIALARSFGVDGVKITDRELLHRDLAAALQSP 551 G +R QE Y R S + + N PDF+ALA+++G G+++ AL + Sbjct: 487 MYGTIRMHQEKAYPGRVSGTSLTN--PDFVALAQAYGALGLRVRRTAEFGPAFDQALVAG 544 Query: 552 TPTMIDVH 559 P +I++H Sbjct: 545 RPVLIEIH 552 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: 999 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: 617 Length of database: 576 Length adjustment: 37 Effective length of query: 580 Effective length of database: 539 Effective search space: 312620 Effective search space used: 312620 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