Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_010876856.1 MTH_RS05875 homoserine dehydrogenase
Query= reanno::Miya:8500664 (436 letters) >NCBI__GCF_000008645.1:WP_010876856.1 Length = 423 Score = 338 bits (868), Expect = 1e-97 Identities = 191/426 (44%), Positives = 262/426 (61%), Gaps = 10/426 (2%) Query: 15 IGMAGFGTVGSGLARVLDENRQWITERTGREMVIKTILVRDLAKPRAWPVPQGATLTADP 74 IG+ GFGT+G+G+ + + N I ++TG E+ ++ ++ D+ R + G L+ D Sbjct: 3 IGLIGFGTIGAGVVEIFNTNPDIIMKKTGMELRLRRVVDLDIETDRGVEIDPGI-LSTDA 61 Query: 75 AVLTDDPEIDVLVELMGGIAAPHAIIKRALEAGKHVVTANKALLAEDGYDLYRLAEQKNV 134 + +DPEID+++EL+GG + I +A+E GKHVVTANKALLA ++ A + V Sbjct: 62 DDILEDPEIDIVIELIGGYEPARSFILKAIENGKHVVTANKALLARHWDEIMDAAREHGV 121 Query: 135 GLHHEASVAGGIPIVQTLKESLAGNRIGSLVGILNGTANYILSEMTSNGLDFATALAQAQ 194 + EASV GGIP+++ L ESLA NRI S+ GI+NGTANYIL+ M S G++F L +AQ Sbjct: 122 RVAFEASVGGGIPVLRALNESLAANRIESIYGIINGTANYILTRMASEGMEFDDVLREAQ 181 Query: 195 ELGYAEADPTLDIEGHDTAHKLVLLIRLAYGMDYPYAELPVQGIAGIDRMDIEFA-RELG 253 LGYAE DPT DIEGHDTA KL++L L +G+ P EL V+GI+ I R DIE+A ELG Sbjct: 182 RLGYAERDPTFDIEGHDTAQKLIILTLLGFGVHVPEDELHVEGISSIRRDDIEYATAELG 241 Query: 254 FRIKLLAQVREVDGKLEAGVFPTLVKHTFLIARVGGAYNAIRLEGNAVGPVFLHGLGAGS 313 +KLLA R DG+LE GV PTLV H L++ V G +N I + G+ GPV +G GAG Sbjct: 242 CSVKLLATARLNDGELELGVTPTLVPHHHLLSSVNGVFNGIYITGDFTGPVMFYGKGAGR 301 Query: 314 LPTASAVLADLMTVA---RGAAPHNTGFQRQVPPRADILPPADAESSYYVRAMVPDNPGV 370 TASAV+AD M +A G+ P G R V D + S YY+R D GV Sbjct: 302 RATASAVVADCMDIAVNPEGSMPTGPGI-RVVESVRDF---SRTSSRYYIRLDAVDRAGV 357 Query: 371 LRDLAGAMADHSISIAQAIQKGQHP-QGVPLVFMTHAAKASAIQGAIAQVQAAGLLLAPP 429 L ++AGA + H ISI QKG H + VP+ +TH A AIQGA++++ + P Sbjct: 358 LHEIAGAFSRHGISIESVTQKGAHEGETVPIYIVTHEASEGAIQGALSEISEIRWVRGEP 417 Query: 430 VCYRVL 435 + R+L Sbjct: 418 LRLRIL 423 Lambda K H 0.319 0.137 0.394 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: 470 Number of extensions: 23 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: 436 Length of database: 423 Length adjustment: 32 Effective length of query: 404 Effective length of database: 391 Effective search space: 157964 Effective search space used: 157964 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 (21.7 bits) S2: 51 (24.3 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