Align 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) (characterized)
to candidate 207060 DVU1609 dihydrodipicolinate reductase
Query= reanno::Miya:8499684 (259 letters) >MicrobesOnline__882:207060 Length = 259 Score = 402 bits (1034), Expect = e-117 Identities = 197/258 (76%), Positives = 223/258 (86%) Query: 1 MSTSIIVTGAGGRMGSTICRMAQEDPVLTLAAVVERPERLASLDVWKCPSGSDPDAVFAT 60 MST IIV GAGGRMGSTICR+ QE+P L LAAV+ERP+R + + C +GSDPD VF Sbjct: 1 MSTPIIVMGAGGRMGSTICRLVQEEPQLCLAAVLERPDRASGVARDGCIAGSDPDVVFPQ 60 Query: 61 VPGGVVVDFTSPEASMANARAAARAGVSHVIGTTGLTAEQKAELADLARTARIFWAPNMS 120 VPGGV++DFT+PEASMA ARAAAR G + VIGTTG EQKAELA+LAR R+FWAPNMS Sbjct: 61 VPGGVIIDFTAPEASMATARAAARHGNAVVIGTTGFNEEQKAELAELARQIRLFWAPNMS 120 Query: 121 IGVNVLLKILPQLVQQLGEQYDLEMVELHHNRKKDSPSGTALRLAECLAEARGWNLPDVA 180 +GVNVLLK+LP+LV+ LGE+YDLEMVELHHNRKKDSPSGTALRLAECLAEAR WNLPDVA Sbjct: 121 VGVNVLLKVLPELVRLLGEKYDLEMVELHHNRKKDSPSGTALRLAECLAEARDWNLPDVA 180 Query: 181 NYHREGIIGERPKDEIGIQTIRGGDVVGVHTIYAMGPGERIEITHQAHSRENFAQGALRA 240 YHREGIIGERP+ EIG+QTIRGGDVVGVHT+Y +GPGERIE+THQAHSRE FAQGALRA Sbjct: 181 CYHREGIIGERPQKEIGVQTIRGGDVVGVHTVYCLGPGERIEVTHQAHSRETFAQGALRA 240 Query: 241 AKWLPQQQPGTLYSMLDM 258 A WL Q+PG LY+M D+ Sbjct: 241 AAWLATQKPGKLYNMADI 258 Lambda K H 0.318 0.133 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: 280 Number of extensions: 4 Number of successful extensions: 1 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: 259 Length of database: 259 Length adjustment: 24 Effective length of query: 235 Effective length of database: 235 Effective search space: 55225 Effective search space used: 55225 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 207060 DVU1609 (dihydrodipicolinate 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.12504.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-80 256.2 0.0 3.9e-80 255.2 0.0 1.4 1 lcl|MicrobesOnline__882:207060 DVU1609 dihydrodipicolinate redu Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:207060 DVU1609 dihydrodipicolinate reductase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 255.2 0.0 3.9e-80 3.9e-80 3 269 .. 4 259 .] 2 259 .] 0.93 Alignments for each domain: == domain 1 score: 255.2 bits; conditional E-value: 3.9e-80 TIGR00036 3 kvavaGaaGrmGrevikavkeaedlelvaalerkgsskqgkDiGelagigkvgvpveddleavkvlaekkadvliDftt 81 ++ v Ga+GrmG+ + + v+e+++l l+a+ler++ + +g+++ g + + + + v + +v+iDft lcl|MicrobesOnline__882:207060 4 PIIVMGAGGRMGSTICRLVQEEPQLCLAAVLERPD---------RASGVARDGC-IAGS-DPDVVFPQVPGGVIIDFTA 71 589*****************************733.........2356666666.3222.223356688899******* PP TIGR00036 82 peavlenvkialekgvrlVvGTTGfseedlkelkdlaekkgvalviapNfaiGvnlllkllekaakvledv.DiEiiEl 159 pea + ++++a+++g +V+GTTGf+ee+++el++la + ++l apN+++Gvn+llk+l ++ + l++ D+E++El lcl|MicrobesOnline__882:207060 72 PEASMATARAAARHGNAVVIGTTGFNEEQKAELAELARQ--IRLFWAPNMSVGVNVLLKVLPELVRLLGEKyDLEMVEL 148 ***************************************..***************************8755******* PP TIGR00036 160 HHrhKkDaPSGTAlklaeiiakargkdlkeaaveeregltGerkkeeiGiaavRggdvvgehtvlFasdGerleitHka 238 HH+ KkD+PSGTAl+lae++a+ar+ +l ++a ++reg+ Ger ++eiG++++Rggdvvg htv+ + Ger+e+tH+a lcl|MicrobesOnline__882:207060 149 HHNRKKDSPSGTALRLAECLAEARDWNLPDVACYHREGIIGERPQKEIGVQTIRGGDVVGVHTVYCLGPGERIEVTHQA 227 ******************************************************************************* PP TIGR00036 239 ssRaafakGvvrairwledkee.kvydledvl 269 +sR++fa+G++ra+ wl+ ++ k+y++ d++ lcl|MicrobesOnline__882:207060 228 HSRETFAQGALRAAAWLATQKPgKLYNMADIF 259 ******************999889*****986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (259 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 2.40 // [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