Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_013553873.1 NITSA_RS04680 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::O67216 (294 letters) >NCBI__GCF_000186245.1:WP_013553873.1 Length = 298 Score = 260 bits (664), Expect = 3e-74 Identities = 132/294 (44%), Positives = 197/294 (67%), Gaps = 5/294 (1%) Query: 1 MFQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIE 60 M G++ ALITPF+ GE+D +LI + +G DA++ GTTGES TL+ +EH++ IE Sbjct: 4 MICGAMTALITPFRNGELDEATYADLIRRQIAHGMDAVVPVGTTGESATLSHDEHKRCIE 63 Query: 61 FAVK--RAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHF 118 AV+ R +G +KVIAG G NATHEA+ + HA+E GA L V PYYNKP+Q GLY+H+ Sbjct: 64 IAVEVCRDSG-VKVIAGAGSNATHEAIDIARHAQECGAHAILSVAPYYNKPSQEGLYQHY 122 Query: 119 KTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLG 178 K +A+ ++IP+++YN+P RT V+I T+F+L E ENI A KE+T +M+R +++ Sbjct: 123 KAIAEAIEIPVMLYNVPGRTSVDIQPATVFRLFDEVENIYAIKEATGSMERAVDLLAARP 182 Query: 179 ESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHD 238 E ++SGDD++ P++A GAKGVISV N++P +L+ AL GD ++ I+ L+ Sbjct: 183 E-LCLVSGDDAIDYPLLANGAKGVISVTANLLPDLKSKLVHTALAGDLAASKAINDSLYP 241 Query: 239 LFKVLFIETNPIPVKTACWMLGMCEK-EFRLPLTEMSPENENKLREVLKKYNLP 291 + K +F+E+NPIPVK A ++ G+ E+RLPL S EN K+ ++ Y +P Sbjct: 242 INKAMFVESNPIPVKAAMYLAGLLPTLEYRLPLVPPSAENMKKIEAAIQNYTIP 295 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: 234 Number of extensions: 10 Number of successful extensions: 4 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: 298 Length adjustment: 26 Effective length of query: 268 Effective length of database: 272 Effective search space: 72896 Effective search space used: 72896 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 WP_013553873.1 NITSA_RS04680 (4-hydroxy-tetrahydrodipicolinate synthase)
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.13102.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-108 348.3 0.1 1.3e-108 348.1 0.1 1.0 1 lcl|NCBI__GCF_000186245.1:WP_013553873.1 NITSA_RS04680 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553873.1 NITSA_RS04680 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 348.1 0.1 1.3e-108 1.3e-108 2 285 .. 8 291 .. 7 292 .. 0.98 Alignments for each domain: == domain 1 score: 348.1 bits; conditional E-value: 1.3e-108 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvkn.rvp 69 +tAliTPf++ + +d a+++ li++qi++g+da+v+vGtTGEsatLs++E+k++ie+ave++++ v+ lcl|NCBI__GCF_000186245.1:WP_013553873.1 8 AMTALITPFRNGE-LDEATYADLIRRQIAHGMDAVVPVGTTGESATLSHDEHKRCIEIAVEVCRDsGVK 75 689******9988.************************************************98746** PP TIGR00674 70 viaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgv 138 viaG+gsnat+eai+++++a+++g++++l+v+PyYnkP+qeGly+h+kaiae++e+P++lYnvP+Rt+v lcl|NCBI__GCF_000186245.1:WP_013553873.1 76 VIAGAGSNATHEAIDIARHAQECGAHAILSVAPYYNKPSQEGLYQHYKAIAEAIEIPVMLYNVPGRTSV 144 ********************************************************************* PP TIGR00674 139 slepetvkrLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnv 206 +++p tv+rL++eve i aiKea+g++er++ + a + ++ + sGdDa+ ++la GakGviSV++n+ lcl|NCBI__GCF_000186245.1:WP_013553873.1 145 DIQPATVFRLFDEVEnIYAIKEATGSMERAVDLLAARP-ELCLVSGDDAIDYPLLANGAKGVISVTANL 212 *************999*******************998.9***************************** PP TIGR00674 207 apkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseek 275 +p++ +++v++al+gd + + i+ l ++ ka+f+e+NPipvK+a++l+gl + e+RlPL++ s e+ lcl|NCBI__GCF_000186245.1:WP_013553873.1 213 LPDLKSKLVHTALAGDLAASKAINDSLYPINKAMFVESNPIPVKAAMYLAGLLPTLEYRLPLVPPSAEN 281 ********************************************************************* PP TIGR00674 276 keklkevlke 285 +k+++++++ lcl|NCBI__GCF_000186245.1:WP_013553873.1 282 MKKIEAAIQN 291 *****99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (298 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.76 // [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