Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_010439268.1 G7G_RS0105370 hypothetical protein
Query= BRENDA::O06335 (552 letters) >NCBI__GCF_000192475.1:WP_010439268.1 Length = 524 Score = 135 bits (340), Expect = 4e-36 Identities = 158/562 (28%), Positives = 237/562 (42%), Gaps = 64/562 (11%) Query: 3 VGDHLVARMRAAGISVVCGLPTSRLDSLLVRLSRDAGFQIVLARHEGGAGYLADGFARAS 62 +G + ++ G+ V+ G+P + + R +AG VLARHE GAG++ADG+ARAS Sbjct: 5 LGAQISHMLKDRGVDVIFGIPGVH-NQEMYRGIEEAGITHVLARHEQGAGFMADGYARAS 63 Query: 63 GKSAAVFV-AGPGATNVISAVANASVNQVPMLILTG---EVAVGEFGLHSQQDTSDDGLG 118 GK +V GPG N+++ + A + VPML+L+ +V LH +D G Sbjct: 64 GKPGVAYVITGPGLCNIMTPMGQAYSDSVPMLVLSSCLDDVQSRRGQLHQMKDQR----G 119 Query: 119 LGATFRRFCRCSVSIESIANARSKIDSAFRALASIPRGPVHIALP-RDLVDERLPAHQLG 177 T + S + + ++ AF P HI +P L E PA Sbjct: 120 AADTVADW---SCQADDAQSTYLLVERAFEDFELSRPRPKHIQIPIAQLEAEAEPAPFPN 176 Query: 178 TAAAGLGGLRTLAPCGPDVADEVIGRLDRSRAPMLVLGNGCRLDGIGEQIVAFCEKAGLP 237 A LRT A PDVA V+ L+ ++ P+ +LG G R + QI+ + G Sbjct: 177 QPA-----LRTKA-LPPDVA-PVLSLLNIAQRPLFILGGGSR-SNLWRQILT---ELGAA 225 Query: 238 FATTPNGRGIVAETHPLSLGVLGIFGDGRADEYLFDTPCDLLIAVGVSFGGLVTRSFSPR 297 TT GRG+V +PL G + + G A+ DL++ VG G + Sbjct: 226 CFTTFAGRGLVGANYPLDFGSM-LPRPGSAEVI---ASADLVVVVGAELGEV------DL 275 Query: 298 WR---GLKADVVHVDPDPSAVGRFVATSLGITTSGRAFVNAL-----------NCGRPPR 343 WR G A +V VD DP + ++ I G +F AL + Sbjct: 276 WRDRLGHSAQLVRVDIDPEVLSDHHRATVKIQADGESFAYALWQSVEKVQPAGGWSQDEV 335 Query: 344 FCRRVGVRPPAPAALPGTPQARGESIHPLELMHELDRELAPNATICADVGTCISWTFRGI 403 R R A LPG Q + + RE P T+ T ++ + I Sbjct: 336 SEARARWRAEINAELPGIVQ-----------VSDALREAMPVETMIYSDMTQFAYVSKEI 384 Query: 404 -PVRRPGRFFATVDFSPMGCGIAGAIGVALARPEEHVICIAGDGAFLMHGTEISTAVAHG 462 + P + F +G + IG A+AR + IAGD F E+ AV G Sbjct: 385 WDMHYPYHWHHPTGFGTLGYALPAGIGGAMARRGKPTAVIAGDYGFHYTMQELGVAVELG 444 Query: 463 IRVTWAVLNDGQMSASAGPVSGRMDPSPVARIGAN-DLAAMARALGAEGIRVDTRCELRA 521 + + + ++G++ A + R +P A I N D +A A GA E++A Sbjct: 445 LPLPIILWDNGKLKAIEDSMV-RSQIAPNAVIARNPDFCKLAEAFGARSAEPGNLDEMQA 503 Query: 522 GVQKALAATGPCVLDIAIDPEI 543 V+KA A GP + I I PEI Sbjct: 504 AVRKAFTANGPTL--IRITPEI 523 Lambda K H 0.322 0.139 0.425 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: 674 Number of extensions: 36 Number of successful extensions: 4 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: 552 Length of database: 524 Length adjustment: 35 Effective length of query: 517 Effective length of database: 489 Effective search space: 252813 Effective search space used: 252813 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 (21.9 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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