Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate WP_013011753.1 DACET_RS12565 4-hydroxy-tetrahydrodipicolinate reductase
Query= BRENDA::Q9K1F1 (269 letters) >NCBI__GCF_000025725.1:WP_013011753.1 Length = 268 Score = 246 bits (627), Expect = 5e-70 Identities = 130/268 (48%), Positives = 173/268 (64%), Gaps = 2/268 (0%) Query: 1 MTPLKIAIAGANGRMGRVLVEAVNNHPDTVLSGALEHSGSEALGLDAGYAVGL-KTGIAI 59 M+ +KIA+ GA G+MGR ++ + L+GALEHS LG DAG G K + I Sbjct: 1 MSKVKIAMVGAAGKMGRRIISLITEDERCELNGALEHSACPFLGHDAGDVAGCGKLSVEI 60 Query: 60 SDDVDAVLAQSDVLIDFTRPEPTLKHLQKCVEKQVNIIIGTTGFDDTGKAAIHTAAEKTG 119 +DD+D DV IDFT EPT+ +L + + V +IG+TG + + + Sbjct: 61 TDDIDKAFDGCDVFIDFTGAEPTMANLSRFQKAGVPAVIGSTGMTTEQTKELEKLSSEMP 120 Query: 120 IVFAANFSVGVNLTFHILDTVARVLNEGYDIEIIEGHHRHKVDAPSGTALRMGEVIAGAL 179 ++F+ N SVGVNLTF IL+ V + + E +DIEIIE HHR K DAPSGTA+RMGEVIA L Sbjct: 121 VLFSPNMSVGVNLTFKILEMVTQAIGETWDIEIIEAHHRMKKDAPSGTAMRMGEVIANVL 180 Query: 180 GRDLKQCAVYGREGHTGPRDPSTIGFATVRAGDIVGDHTALFATDGERVEITHKASSRMT 239 GRD+++ + R G G R IG T+RAGDIVG+HTA+F T+GER+EITH+A +R Sbjct: 181 GRDIEKDGAFCRHGLIGERTDREIGMQTLRAGDIVGEHTAMFCTNGERIEITHRAHTRDM 240 Query: 240 FAAGAVRAAVWVNGK-TGLYDMQDVLGL 266 FA GA+ AAVW+ G+ G Y+M DVLGL Sbjct: 241 FAKGAISAAVWLKGRDNGFYNMFDVLGL 268 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: 256 Number of extensions: 9 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: 268 Length adjustment: 25 Effective length of query: 244 Effective length of database: 243 Effective search space: 59292 Effective search space used: 59292 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 WP_013011753.1 DACET_RS12565 (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.1439.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.3e-93 296.8 1.8 9.3e-93 296.6 1.8 1.0 1 lcl|NCBI__GCF_000025725.1:WP_013011753.1 DACET_RS12565 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025725.1:WP_013011753.1 DACET_RS12565 4-hydroxy-tetrahydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 296.6 1.8 9.3e-93 9.3e-93 2 270 .] 4 267 .. 3 267 .. 0.99 Alignments for each domain: == domain 1 score: 296.6 bits; conditional E-value: 9.3e-93 TIGR00036 2 ikvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlae 70 +k+a+ GaaG+mGr++i ++e e el +ale + + g+D+G++ag+gk+ v+++dd++ + lcl|NCBI__GCF_000025725.1:WP_013011753.1 4 VKIAMVGAAGKMGRRIISLITEDERCELNGALEHSACPFLGHDAGDVAGCGKLSVEITDDIDKA----F 68 79************************************************************77....9 PP TIGR00036 71 kkadvliDfttpeavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlll 139 + +dv+iDft +e ++ n+ ++gv V+G TG++ e++kel++l+++ ++++++pN+++Gvnl + lcl|NCBI__GCF_000025725.1:WP_013011753.1 69 DGCDVFIDFTGAEPTMANLSRFQKAGVPAVIGSTGMTTEQTKELEKLSSE--MPVLFSPNMSVGVNLTF 135 9*************************************************..***************** PP TIGR00036 140 kllekaakvledv.DiEiiElHHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeei 207 k+le++++ +++ DiEiiE+HHr KkDaPSGTA++++e+ia++ g+d++++ +r+gl Ger++ ei lcl|NCBI__GCF_000025725.1:WP_013011753.1 136 KILEMVTQAIGETwDIEIIEAHHRMKKDAPSGTAMRMGEVIANVLGRDIEKDGAFCRHGLIGERTDREI 204 **********9977******************************************************* PP TIGR00036 208 GiaavRggdvvgehtvlFasdGerleitHkassRaafakGvvrairwledkeekvydledvld 270 G++++R+gd+vgeht +F ++Ger+eitH+a+ R++fakG++ a+ wl+ ++++y++ dvl+ lcl|NCBI__GCF_000025725.1:WP_013011753.1 205 GMQTLRAGDIVGEHTAMFCTNGERIEITHRAHTRDMFAKGAISAAVWLKGRDNGFYNMFDVLG 267 *************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (268 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: 00:00:00.00 # Mc/sec: 8.32 // [ok]
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