Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_017549759.1 C792_RS0112315 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase
Query= BRENDA::O67216 (294 letters) >NCBI__GCF_000330705.1:WP_017549759.1 Length = 302 Score = 251 bits (640), Expect = 2e-71 Identities = 131/287 (45%), Positives = 183/287 (63%), Gaps = 1/287 (0%) Query: 3 QGSIVALITPFKE-GEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEF 61 +GSI +ITPFKE G++D++ LIE+ +DNGT I V GT+GE +LT +E +++E Sbjct: 13 RGSICPVITPFKENGDIDFDGQAGLIEYQLDNGTHCISVTGTSGEPSSLTTKERVQIMEH 72 Query: 62 AVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTV 121 A+K AGR+ GTG E ++LT A+E+GAD A+V+VPYYNKP Q LY+HFKTV Sbjct: 73 AMKTIAGRVPFAPGTGSVNHDETMYLTKKAEEMGADAAMVIVPYYNKPNQDALYDHFKTV 132 Query: 122 AQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESF 181 A V IPIIIYNIP RT + ++ TM +L+ +C NIV KES + + ++ ++ G F Sbjct: 133 ADAVAIPIIIYNIPGRTALNMTAGTMARLSRDCPNIVGVKESNKDFEHVNRVMLNCGRDF 192 Query: 182 SVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFK 241 + SG + L PM+A+G G IS NV PR+V E+ A GD RA ++HY L +L Sbjct: 193 LLYSGIELLCYPMLAIGGAGSISATANVEPRKVAEMHDAWERGDRDRALDLHYELMNLND 252 Query: 242 VLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKY 288 VLF +TNP PVK A M+G E R P+ S + + ++RE L+ Y Sbjct: 253 VLFKDTNPAPVKAALGMMGKIEPVLRKPMGMPSSKLQEEIRETLRTY 299 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: 243 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: 294 Length of database: 302 Length adjustment: 26 Effective length of query: 268 Effective length of database: 276 Effective search space: 73968 Effective search space used: 73968 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_017549759.1 C792_RS0112315 (2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase)
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.3868302.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-89 286.0 0.0 1.3e-89 285.8 0.0 1.0 1 NCBI__GCF_000330705.1:WP_017549759.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000330705.1:WP_017549759.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 285.8 0.0 1.3e-89 1.3e-89 2 285 .. 15 298 .. 14 299 .. 0.99 Alignments for each domain: == domain 1 score: 285.8 bits; conditional E-value: 1.3e-89 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 ++ +iTPfke+g++df+ + lie+q+++g+ i v Gt GE +L+++E+++++e a+++ ++rvp Gt NCBI__GCF_000330705.1:WP_017549759.1 15 SICPVITPFKENGDIDFDGQAGLIEYQLDNGTHCISVTGTSGEPSSLTTKERVQIMEHAMKTIAGRVPFAPGT 87 67789******************************************************************** PP TIGR00674 75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkr 147 gs + +e++ ltk+ae++g+d+++v++PyYnkP+q ly hfk++a++v +Pii+Yn+P+Rt+ +++ t++r NCBI__GCF_000330705.1:WP_017549759.1 88 GSVNHDETMYLTKKAEEMGADAAMVIVPYYNKPNQDALYDHFKTVADAVAIPIIIYNIPGRTALNMTAGTMAR 160 ************************************************************************* PP TIGR00674 148 Laeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaal 219 L+++++ iv++Ke+++d e+v++++ + df ++sG + l ++la+G++G iS ++nv p++++em a+ NCBI__GCF_000330705.1:WP_017549759.1 161 LSRDCPnIVGVKESNKDFEHVNRVMLNCGRDFLLYSGIELLCYPMLAIGGAGSISATANVEPRKVAEMHDAWE 233 ****999****************************************************************** PP TIGR00674 220 egdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlke 285 +gd ++a+ +h++l++l ++lf +tNP pvK+al ++g ie lR P+ s++ +e+++e+l++ NCBI__GCF_000330705.1:WP_017549759.1 234 RGDRDRALDLHYELMNLNDVLFKDTNPAPVKAALGMMGKIEP-VLRKPMGMPSSKLQEEIRETLRT 298 *****************************************9.*******************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (302 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 17.76 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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