Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate WP_012408685.1 NPUN_RS10365 thiamine pyrophosphate-binding protein
Query= BRENDA::P9WG41 (618 letters) >NCBI__GCF_000020025.1:WP_012408685.1 Length = 568 Score = 172 bits (437), Expect = 3e-47 Identities = 158/565 (27%), Positives = 242/565 (42%), Gaps = 32/565 (5%) Query: 39 TGAQAVIRSLEELGVDVIFGIPGGAVLPVYDPLFDSKKLRHVLVRHEQGAGHAASGYAHV 98 TG A++ G+ +FG PG + D + + L+++L E A AA GYA Sbjct: 5 TGRFAILEQFLADGIHYMFGNPGTSEEGFLDAIREYPDLKYILTLQESVAVMAADGYARA 64 Query: 99 TGRVGVCMATSGPGATNLVTPLADAQMDSIPVVAITGQVGRGLIGTDAFQEADISGITMP 158 T + + S PG N + L A P+V I G G DA D+ P Sbjct: 65 TKKPALVQIHSTPGLGNAIGALYQAYRGHSPLVVIGGDAGIKYQAMDAQMAGDLVAFAEP 124 Query: 159 ITKHNFLVRSGDDIPRVLAEAFHIAASGRPGAVLVDIPKDVLQGQCTFSWPPRME--LPG 216 +TK + +V + RVL A IAA+ G V V +P D+L P +E P Sbjct: 125 VTKWSTMVMEPSSLLRVLRRAIKIAATPPMGPVYVCLPVDILDA-------PAVEEVRPT 177 Query: 217 YKPNTK--PHSRQVREAAKLIAAARKPVLYVGGGVIRGEATEQLRELAELTGIPVVTTLM 274 P+TK P ++ AA ++A+A KP+++VG GV A ++L +AEL G V Sbjct: 178 SIPSTKVLPDEELLKTAATMLASAHKPMIFVGDGVAYSSAQDELTRVAELLGAEVWEVDA 237 Query: 275 ARGAFPDSHRQNLGMPGMHGTVAAVAALQRSDLLIALGTRFDDRVTGKLDS-FAPEAKVI 333 +H GM G + R D+ + GT V +L + FAP AKVI Sbjct: 238 GELNMSHAHPLYQGMTGHMFGYQSRPITNRGDVNLVCGTYLLPEVFPELGNIFAPGAKVI 297 Query: 334 HADIDPAEIGKNRHADVPIVGDVKAVITELIAMLRHHHIPGTIEMADWWAYLNGVRKTYP 393 H D++ EI KN D+ +V D K + L +L E A K Sbjct: 298 HIDLNAYEIAKNHSVDLGLVSDPKLTLAHLAKVLSAVMTSEQKETAKTRTADIAQAKEEN 357 Query: 394 LSYGPQSD---GSLSPEYVIEKLGEIAGPDAVFVAGVGQHQMWAAQFIRY---EKPRSWL 447 Q+D P + E+A V + + RY KP + Sbjct: 358 HKRELQADRENWDAVPLHFSRFAAELAKQLPEDVIIFDEALTCSPDLTRYLPPTKPGHYF 417 Query: 448 NSGGLGTMGFAIPAAMGAKIALPGTEVWAIDGDGCFQMTNQELATCAVEGIPVKVALINN 507 S G G++G IP +GAK+A P T V GDG T Q L + A I K + NN Sbjct: 418 LSRG-GSLGVGIPGTIGAKLANPDTTVIGFTGDGAAMYTIQALWSAARHNIDAKFVICNN 476 Query: 508 GNLGMVRQWQSLFYAERYSQTDLATHSHRIP--------DFVKLAEALGCVGLRCEREED 559 + +++ ++ ER D+ H + + +FV++A ++G G+R E+ ++ Sbjct: 477 HSYRLLQVNIQAYWQER----DIPQHEYPLSFDLSKPEINFVEIARSMGVEGVRLEKAQE 532 Query: 560 VVDVINQARAINDCPVVIDFIVGAD 584 + + QA A + P +ID ++ A+ Sbjct: 533 IAPALEQALA-HKGPFLIDVVLEAN 556 Lambda K H 0.319 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: 894 Number of extensions: 43 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 618 Length of database: 568 Length adjustment: 37 Effective length of query: 581 Effective length of database: 531 Effective search space: 308511 Effective search space used: 308511 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