Align homoserine dehydrogenase (EC 1.1.1.3) (characterized)
to candidate WP_078429990.1 BK574_RS21130 homoserine dehydrogenase
Query= BRENDA::D8WXQ1 (432 letters) >NCBI__GCF_002019605.1:WP_078429990.1 Length = 433 Score = 602 bits (1552), Expect = e-177 Identities = 293/428 (68%), Positives = 359/428 (83%) Query: 1 MEAIQVGLLGLGTVGSGVVKIIENHQDKLMHQVGCPVKVKKILVQDLNKKRDVDVDPAQL 60 + I +GLLGLGTVG+GV+KIIE HQ++LMH+VGCPV V K+LV+ L KKR+V +D +L Sbjct: 4 VNGISIGLLGLGTVGTGVIKIIEGHQEELMHKVGCPVTVGKVLVRSLEKKRNVQIDENKL 63 Query: 61 TTNADDILQDPDIDVVIEVMGGIEETRNYLLKALSEKKHVVTANKDLMAVYGSELLTAAS 120 T N +DI+ +P++D+VIEVMGG++E ++Y+++AL KKHVVTANKDLMA+YG+ELL A Sbjct: 64 TENPEDIIDNPNVDIVIEVMGGVKEAKSYIVRALQNKKHVVTANKDLMALYGAELLQIAQ 123 Query: 121 ANGCDLFYEASVAGGIPILRSLVDGLASDRITKMMGIVNGTTNYILTKMSKHGRAYEEVL 180 NGCDL+YEASVAGGIPI+RSL +GLASDRITKMMGIVNGTTN+ILTKMSK G +YE+VL Sbjct: 124 DNGCDLYYEASVAGGIPIIRSLSEGLASDRITKMMGIVNGTTNFILTKMSKQGSSYEDVL 183 Query: 181 KEAQELGYAEADPASDVEGLDAARKMAILATLGFSMKIDLDDVKVEGITRITEEDIQYGK 240 KEAQELG+AE+DP SDVEGLDAARKM+ILATLGFSM + L+DV V GIT +T++D+ Y Sbjct: 184 KEAQELGFAESDPTSDVEGLDAARKMSILATLGFSMNVGLEDVVVRGITTVTQDDLHYCD 243 Query: 241 QLGYTMKLIGIAHREGEKVEVSVQPTLLSDSHPLASVNDEYNAVYVYGEAVGETMFYGPG 300 LGYTMKLIG+A R +VEVSVQPTLL HPLASVNDEYNAVYVYGEAVGETMFYGPG Sbjct: 244 HLGYTMKLIGLAQRNEGRVEVSVQPTLLPSEHPLASVNDEYNAVYVYGEAVGETMFYGPG 303 Query: 301 AGSLPTATAVVSDLVGVMKNMRLGVNGANAVTPQYQKKLKGPDEIYSKFFLRLHVKDEVG 360 AGSLPTATA+VSDLV VMKNMRLGV G + TP Y K+LK +EI SK+FLRLHV D+ G Sbjct: 304 AGSLPTATAIVSDLVTVMKNMRLGVTGRHITTPLYHKELKSDEEIQSKYFLRLHVVDKAG 363 Query: 361 VFANITSIFSEHSVSFEKILQMPLKENGLAEIVLVTHQASLQDYEDILVKLRDLNAVHEI 420 F+ ITS+F+EH VSFEK+LQ+P+K + L+EI+++TH S + YE+I L L+ VH + Sbjct: 364 TFSAITSLFAEHGVSFEKLLQLPIKGSNLSEIIIITHTTSKRTYEEIYQALDQLDVVHSV 423 Query: 421 KSSYRVEG 428 +SSYRVEG Sbjct: 424 QSSYRVEG 431 Lambda K H 0.316 0.134 0.368 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: 628 Number of extensions: 18 Number of successful extensions: 2 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: 432 Length of database: 433 Length adjustment: 32 Effective length of query: 400 Effective length of database: 401 Effective search space: 160400 Effective search space used: 160400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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