Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate 8499797 DvMF_0562 dihydrodipicolinate synthase (RefSeq)
Query= BRENDA::O67216 (294 letters) >FitnessBrowser__Miya:8499797 Length = 292 Score = 302 bits (774), Expect = 5e-87 Identities = 139/284 (48%), Positives = 200/284 (70%) Query: 2 FQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEF 61 FQG+ AL+TPF+ GEVD E L+E+ ++ G + ++ CGTTGES TLT +EH+ VI Sbjct: 3 FQGAFTALVTPFRNGEVDEERYRALVEWQIEQGINGLVPCGTTGESATLTHQEHKDVIRI 62 Query: 62 AVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTV 121 V++ GR+ V+AG G N T EAV LT +AK+ GADGAL++ PYYNKPTQ GLY+HFK + Sbjct: 63 CVEQVKGRVPVLAGAGSNNTREAVELTRYAKQAGADGALLITPYYNKPTQEGLYQHFKAI 122 Query: 122 AQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESF 181 A EV +P I+YN+PSRT + +T+ ++ + ++ KE+T N+ ++SEI++ G F Sbjct: 123 AAEVPMPFIVYNVPSRTGTNLCPETLARMKRDIPEVIGVKEATGNLIQVSEIIEYCGADF 182 Query: 182 SVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFK 241 VLSGDD LP++A+G GVISV++NV+P ++ EL RA EGD AR +HY + + + Sbjct: 183 QVLSGDDFTVLPLLAVGGCGVISVSSNVVPAKMSELCRAFFEGDLATARRVHYEIASINR 242 Query: 242 VLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVL 285 +F+ETNPIPVKTA M+G E E RLP+ + P N+++LR++L Sbjct: 243 AMFLETNPIPVKTALSMMGRIELELRLPMVPLQPANQSRLRDIL 286 Lambda K H 0.318 0.136 0.390 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: 263 Number of extensions: 7 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: 294 Length of database: 292 Length adjustment: 26 Effective length of query: 268 Effective length of database: 266 Effective search space: 71288 Effective search space used: 71288 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: 48 (23.1 bits)
Align candidate 8499797 DvMF_0562 (dihydrodipicolinate synthase (RefSeq))
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
# 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/TIGR00674.hmm # target sequence database: /tmp/gapView.28307.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00674 [M=286] Accession: TIGR00674 Description: dapA: 4-hydroxy-tetrahydrodipicolinate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.8e-116 371.9 0.0 8.8e-116 371.7 0.0 1.0 1 lcl|FitnessBrowser__Miya:8499797 DvMF_0562 dihydrodipicolinate sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8499797 DvMF_0562 dihydrodipicolinate synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 371.7 0.0 8.8e-116 8.8e-116 2 284 .. 6 287 .. 5 289 .. 0.99 Alignments for each domain: == domain 1 score: 371.7 bits; conditional E-value: 8.8e-116 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtgsna 78 tAl+TPf++ + vd + + l+e qie+g++++v++GtTGEsatL+++E+k+vi++ ve vk+rvpv+aG+gsn+ lcl|FitnessBrowser__Miya:8499797 6 AFTALVTPFRNGE-VDEERYRALVEWQIEQGINGLVPCGTTGESATLTHQEHKDVIRICVEQVKGRVPVLAGAGSNN 81 579******9888.*************************************************************** PP TIGR00674 79 teeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrLaeeve.i 154 t+ea+elt+ a+++g+dg+l++tPyYnkPtqeGly+hfkaia+ev +P i+YnvPsRtg++l pet++r+ ++ + + lcl|FitnessBrowser__Miya:8499797 82 TREAVELTRYAKQAGADGALLITPYYNKPTQEGLYQHFKAIAAEVPMPFIVYNVPSRTGTNLCPETLARMKRDIPeV 158 ***********************************************************************99888* PP TIGR00674 155 vaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaalegdteeareihq 231 +++Kea+g+l +vsei+++ ++df+vlsGdD ++l++la+G++GviSV snv+p +++e+++a+ egd + ar +h+ lcl|FitnessBrowser__Miya:8499797 159 IGVKEATGNLIQVSEIIEYCGADFQVLSGDDFTVLPLLAVGGCGVISVSSNVVPAKMSELCRAFFEGDLATARRVHY 235 ***************************************************************************** PP TIGR00674 232 kllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlk 284 ++ ++ +a+f+etNPipvKtal ++g ie elRlP+++l+ ++++l+++l+ lcl|FitnessBrowser__Miya:8499797 236 EIASINRAMFLETNPIPVKTALSMMGRIEL-ELRLPMVPLQPANQSRLRDILS 287 ******************************.********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (292 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.36 // [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