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_011652827.1 RL_RS17185 thiamine pyrophosphate-binding protein
Query= SwissProt::P0DP90 (548 letters) >NCBI__GCF_000009265.1:WP_011652827.1 Length = 552 Score = 242 bits (617), Expect = 3e-68 Identities = 168/535 (31%), Positives = 263/535 (49%), Gaps = 18/535 (3%) Query: 3 GAQWVVHALRAQGVNTVFGYPGGAIMPVYDALYDGGVEHLLCRHEQGAAMAAIGYARATG 62 G + +V AL+A GV + PG + + V DAL D ++ L+CR E GAAM A + R TG Sbjct: 5 GGELIVEALKANGVQRLSCVPGESFLAVLDALRDSDIDVLVCRQEGGAAMMADCWGRLTG 64 Query: 63 KTGVCIATSGPGATNLITGLADALLDSIPVVAITGQVSAPFIGTDAFQEVDVLGLSLACT 122 + G+C+ T GPGATN GL A DSIP++ GQV +AFQEV+ Sbjct: 65 EPGICMVTRGPGATNASAGLHIAKQDSIPMILFIGQVQREAREREAFQEVEFRRAFTEFA 124 Query: 123 KHSFLVQSLEELPRIMAEAFDVACSGRPGPVLVDIPKDIQLASGDLEPWFTTVENEVTFP 182 K + +P + AF VA SGRPGPV++ +P+D+ L P N P Sbjct: 125 KWVGEIDDAARIPEFVTRAFAVATSGRPGPVVLTLPEDM-LRDEVEAPRARHYANVEAHP 183 Query: 183 -HAEVEQARQMLAKAQKPMLYVGGGVGMAQAVPALREFLAATKMPATCTLKGLGAVEADY 241 +++ L KA++PM +GG A AV + F ++P C+ + + + Sbjct: 184 GRRQIDDFYLRLLKAERPMAILGGTRWDADAVADFQSFAERFQLPIGCSFRRQMLFDHLH 243 Query: 242 PYYLGMLGMHGTKAANFAVQECDLLIAVGARFDDRVTGK---LNTFAPHASVIHMDIDPA 298 P Y G +G+ A ++E DLLI +G+R + + ++ P S++H+ D + Sbjct: 244 PCYAGDVGIGINPALAKEIKESDLLILLGSRMSEMPSSSYTLIDIPYPQQSLVHIYPDAS 303 Query: 299 EMNKLRQAHVAL---QGDLNALLPALQQPLNQYDWQQHCAQLRDEH-SWR---YDHPGDA 351 E+ ++ + +A+ D A L L+ P + W + A+L + +W PG A Sbjct: 304 ELGRIYRPDLAICAAPADFVAALADLEAPAEPH-WAERTARLHQAYLAWSKPPLSGPG-A 361 Query: 352 IYAPLLLKQLSDRKPADCVVTTDVGQHQMWAAQHIAHT-RPENFITSSGLGTMGFGLPAA 410 ++ +++ L + + T G + W H H R N + G+MG+GLPAA Sbjct: 362 VHMGPIMEWLEANTGPETIFTNGAGNYATWV--HRFHRFRRFNTQAAPTSGSMGYGLPAA 419 Query: 411 VGAQVARPNDTVVCISGDGSFMMNVQELGTVKRKQLPLKIVLLDNQRLGMVRQWQQLFFQ 470 V A+ P V+C +GDG F+M+ QE T R LP+ V+++N G +R Q+ + Sbjct: 420 VAAKRLFPEREVICFAGDGCFLMHGQEFATAIRYGLPIIAVVVNNGIYGTIRMHQEREYP 479 Query: 471 ERYSETTLTDNPDFLMLASAFGIHGQHITRKDQVEAALDTMLNSDGPYLLHVSID 525 R S T LT NPDF LA A+G HG+ + A + S P ++ + +D Sbjct: 480 GRVSSTDLT-NPDFAALARAYGGHGETVETTADFAPAFERARASGKPAIIEIKLD 533 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: 731 Number of extensions: 35 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: 548 Length of database: 552 Length adjustment: 36 Effective length of query: 512 Effective length of database: 516 Effective search space: 264192 Effective search space used: 264192 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