Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate RR42_RS17550 RR42_RS17550 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q9K1F1 (269 letters) >FitnessBrowser__Cup4G11:RR42_RS17550 Length = 265 Score = 331 bits (849), Expect = 9e-96 Identities = 167/264 (63%), Positives = 204/264 (77%), Gaps = 1/264 (0%) Query: 4 LKIAIAGANGRMGRVLVEAVNNHPDTVLSGALEHSGSEALGLDAGYAVGLKTGIAISDDV 63 + IAIAGA+GRMGR+L+E V LSGAL+ G+ ALG DAG +G TG+ I+ D+ Sbjct: 1 MNIAIAGASGRMGRMLIEHVLATEGVTLSGALDVPGAPALGQDAGLLLGRATGVVITSDI 60 Query: 64 DAVLAQSDVLIDFTRPEPTLKHLQKCVEKQVNIIIGTTGFDDTGKAAIHTAAEKTGIVFA 123 +A LA +D LIDFTRPE TL HL V ++ GTTGFDD G+AAI AA+ G+VF+ Sbjct: 61 EAALAGADCLIDFTRPEGTLVHLAAARRLGVKVVTGTTGFDDAGRAAIAEAAKHIGVVFS 120 Query: 124 ANFSVGVNLTFHILDTVARVLNEGYDIEIIEGHHRHKVDAPSGTALRMGEVIAGALGRDL 183 AN SVGVN TF +L+ A++L+ GYDIE+IE HHRHKVDAPSGTAL MGEV+A ALGRDL Sbjct: 121 ANMSVGVNATFKLLEVAAKLLSSGYDIEVIEAHHRHKVDAPSGTALAMGEVVAKALGRDL 180 Query: 184 KQCAVYGREGHTGPRDPSTIGFATVRAGDIVGDHTALFATDGERVEITHKASSRMTFAAG 243 K C V+ REGHTGPRDP++IGFATVR GDIVGDHT +FA GER+EITHK+SSR ++A G Sbjct: 181 KTCGVFAREGHTGPRDPNSIGFATVRGGDIVGDHTVMFAGTGERIEITHKSSSRQSYAEG 240 Query: 244 AVRAAVWVNGK-TGLYDMQDVLGL 266 A+RAA ++ K TGL+DMQDVLGL Sbjct: 241 ALRAARFLADKPTGLFDMQDVLGL 264 Lambda K H 0.318 0.136 0.392 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: 293 Number of extensions: 11 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: 269 Length of database: 265 Length adjustment: 25 Effective length of query: 244 Effective length of database: 240 Effective search space: 58560 Effective search space used: 58560 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate RR42_RS17550 RR42_RS17550 (4-hydroxy-tetrahydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00036.hmm # target sequence database: /tmp/gapView.27090.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00036 [M=270] Accession: TIGR00036 Description: dapB: 4-hydroxy-tetrahydrodipicolinate reductase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-99 318.0 2.5 3.2e-99 317.8 2.5 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS17550 RR42_RS17550 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS17550 RR42_RS17550 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 317.8 2.5 3.2e-99 3.2e-99 2 270 .] 1 263 [. 1 263 [. 0.98 Alignments for each domain: == domain 1 score: 317.8 bits; conditional E-value: 3.2e-99 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlae 70 +++a+aGa+GrmGr +i++v ++e++ l++al+++g + g+D+G l g + gv +++d+ea+ lcl|FitnessBrowser__Cup4G11:RR42_RS17550 1 MNIAIAGASGRMGRMLIEHVLATEGVTLSGALDVPGAPALGQDAGLLLGRAT-GVVITSDIEAA----L 64 789**********************************************985.676******88....7 PP TIGR00036 71 kkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlll 139 ad+liDft+pe++l ++++a + gv++V GTTGf+++++++++++a++ +++v+++N+++Gvn + lcl|FitnessBrowser__Cup4G11:RR42_RS17550 65 AGADCLIDFTRPEGTLVHLAAARRLGVKVVTGTTGFDDAGRAAIAEAAKH--IGVVFSANMSVGVNATF 131 899***********************************************..***************** PP TIGR00036 140 kllekaakvled.vDiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeei 207 klle aak l+ +DiE+iE+HHrhK+DaPSGTAl+++e++aka g+dlk++ v reg+tG r ++i lcl|FitnessBrowser__Cup4G11:RR42_RS17550 132 KLLEVAAKLLSSgYDIEVIEAHHRHKVDAPSGTALAMGEVVAKALGRDLKTCGVFAREGHTGPRDPNSI 200 **********8636******************************************************* PP TIGR00036 208 GiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 G+a+vRggd+vg+htv+Fa+ Ger+eitHk+ssR+++a+G++ra+r+l+dk ++++d++dvl+ lcl|FitnessBrowser__Cup4G11:RR42_RS17550 201 GFATVRGGDIVGDHTVMFAGTGERIEITHKSSSRQSYAEGALRAARFLADKPTGLFDMQDVLG 263 *************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (265 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.79 // [ok]
This GapMind analysis is from Apr 09 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