Align Acetolactate synthase isozyme 2 large subunit; AHAS-II; ALS-II; Acetohydroxy-acid synthase II large subunit; EC 2.2.1.6 (characterized)
to candidate WP_015820176.1 TERTU_RS14925 thiamine pyrophosphate-binding protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000023025.1:WP_015820176.1 Length = 610 Score = 206 bits (524), Expect = 2e-57 Identities = 173/579 (29%), Positives = 263/579 (45%), Gaps = 53/579 (9%) Query: 4 AQWVVHALRAQGVNTVFGYPGGAIMPVYDALYD----GGVEHLLCRHEQGAAMAAIGYAR 59 A ++H L A GV+ VFG PGGAI P+Y+AL G V + HE AA A GY R Sbjct: 22 ADLIIHYLEAIGVDHVFGVPGGAIEPIYNALARSARRGSVAAVGACHEAAAAYMADGYFR 81 Query: 60 ATGKTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQE-----VDV 114 +GK GVC+ATSGPGATNLITG+A A ++IP++ I+GQ + G A QE V+V Sbjct: 82 ESGKLGVCMATSGPGATNLITGVACAYDNNIPMLVISGQPTITSFGKGALQESSCTGVNV 141 Query: 115 LGLSLACTKHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTT 174 +G+ CTK+ LV + +L + A A GPV + +P DI A Sbjct: 142 MGMFRHCTKYDSLVSHINQLETKLVTAILQALQSPQGPVHLSVPVDILRAPVAKPIRALQ 201 Query: 175 VENEV-----TFPHAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATC 229 ++N++ +F + V+ L +P+ +VG G A AV + E + Sbjct: 202 LKNQIEYQNRSFDESAVDALFDELMDDPEPLFFVGNGA--AGAVDKIMELVDICGARFIS 259 Query: 230 TLKGLGAVEADYPYYLGMLGMHGTKAANFAVQE-CDLLIAVGARFDDRVTGKLNTFAPHA 288 G V + Y G+ G+ G +A A+ E ++A G F + +G + Sbjct: 260 APDAKGLVNIRHASYRGVFGLGGHASAVQAIHEHASSIVAFGTGFGEFTSGGWDDALLSD 319 Query: 289 SVIHMDIDPAEMNKLRQAHVALQGDLNALLPALQQPL---------NQYDWQQHCAQLRD 339 +IH+D A + + A + +QG + L L + L N +++ + Sbjct: 320 RLIHVDQSTANLVQSPMAKLHVQGHIPTLCRKLLERLAAAGRVADPNPRYYEKTNPNVTV 379 Query: 340 EHSWRYDHPGDAIYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHTRPENFITSS- 398 + + +Y I L+K LS+ P D G MWA ++ P + + Sbjct: 380 QDASKYHSDEVPIKPQRLMKCLSESFPGHTRFVADAGNSMMWAPHYLQLIDPRQRLNPAA 439 Query: 399 ----------------------GLGTMGFGLPAAVGAQVARPNDTVVCISGDGSFMMNVQ 436 MG+ + AAVG A P VVCI+GDGS++M+ Q Sbjct: 440 ANLANSGNERRRKQSNWLQLTLNFAPMGWAIGAAVGMSRANPRAPVVCITGDGSYLMSGQ 499 Query: 437 ELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQERYSETTLTDNPDFLMLASAFGIHGQ 496 E+ +++LP+ V+L++ GMV Q+L E T DF LA++ GI Sbjct: 500 EITVAAKEKLPVTFVILNDSVYGMVMHGQRLAGAEPIGFELPT--IDFAKLAASMGIRNY 557 Query: 497 HI-TRKDQVEAALDTMLNSDGPYLLHVSIDELENVWPLV 534 I + +D + A GP LL V ID+ E V P++ Sbjct: 558 VIHSAQDFEKIAGGFRALDQGPLLLDVRIDK-EEVPPMI 595 Lambda K H 0.320 0.135 0.410 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: 778 Number of extensions: 43 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: 548 Length of database: 610 Length adjustment: 36 Effective length of query: 512 Effective length of database: 574 Effective search space: 293888 Effective search space used: 293888 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