Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_013135926.1 ARNIT_RS10590 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::O67216 (294 letters) >NCBI__GCF_000092245.1:WP_013135926.1 Length = 295 Score = 269 bits (688), Expect = 5e-77 Identities = 134/289 (46%), Positives = 194/289 (67%), Gaps = 3/289 (1%) Query: 4 GSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFAV 63 G++ ALITPFK G+VD LI+ + G DA++ GTTGES TL+ EH++ IE AV Sbjct: 6 GAMTALITPFKNGKVDASCYEYLIKRQIAQGIDAVVPVGTTGESATLSHNEHKECIEIAV 65 Query: 64 KRAAG-RIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVA 122 G +KVIAG G NATHEA + HA+ VGADG L V PYYNKP Q GLY+H+K +A Sbjct: 66 SVCKGTNVKVIAGAGSNATHEACDIAKHAQNVGADGILSVAPYYNKPMQEGLYQHYKAIA 125 Query: 123 QEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFS 182 + V+IP+++YN+P RT V+I DT +L + +NI A KE+T +++R E+ + + F Sbjct: 126 ESVEIPVMLYNVPGRTGVDIEADTAIRLFDDIKNIYAIKEATGSLERAIELNAKRAD-FC 184 Query: 183 VLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKV 242 V+SGDD + PM+A G+KG+ISV N++P +L+++ EGD+ R I+ L+ L K+ Sbjct: 185 VVSGDDLIDFPMLANGSKGIISVTANLLPNYKSKLVKSVFEGDYETGRAINNELYALNKI 244 Query: 243 LFIETNPIPVKTACWMLGMCEK-EFRLPLTEMSPENENKLREVLKKYNL 290 +F E NPIP+K A ++ G+ + E+RLPLT+ S EN K+ E++K Y + Sbjct: 245 MFCENNPIPIKAAMYIAGLMDTLEYRLPLTKPSLENMKKIEEIIKNYEV 293 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: 270 Number of extensions: 13 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: 295 Length adjustment: 26 Effective length of query: 268 Effective length of database: 269 Effective search space: 72092 Effective search space used: 72092 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_013135926.1 ARNIT_RS10590 (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.24272.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-111 357.4 0.4 2.3e-111 357.2 0.4 1.0 1 lcl|NCBI__GCF_000092245.1:WP_013135926.1 ARNIT_RS10590 4-hydroxy-tetrahyd Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092245.1:WP_013135926.1 ARNIT_RS10590 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 357.2 0.4 2.3e-111 2.3e-111 2 285 .. 7 290 .. 6 291 .. 0.98 Alignments for each domain: == domain 1 score: 357.2 bits; conditional E-value: 2.3e-111 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvkn.rvp 69 +tAliTPfk+ + vd +++e li++qi++g+da+v+vGtTGEsatLs++E+k++ie+av ++k+ v+ lcl|NCBI__GCF_000092245.1:WP_013135926.1 7 AMTALITPFKNGK-VDASCYEYLIKRQIAQGIDAVVPVGTTGESATLSHNEHKECIEIAVSVCKGtNVK 74 689*******998.*************************************************9867** PP TIGR00674 70 viaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgv 138 viaG+gsnat+ea +++k+a+++g+dg+l+v+PyYnkP qeGly+h+kaiae+ve+P++lYnvP+Rtgv lcl|NCBI__GCF_000092245.1:WP_013135926.1 75 VIAGAGSNATHEACDIAKHAQNVGADGILSVAPYYNKPMQEGLYQHYKAIAESVEIPVMLYNVPGRTGV 143 ********************************************************************* PP TIGR00674 139 slepetvkrLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnv 206 ++e +t++rL+++ + i aiKea+g+ler+ e+ a+ +df v sGdD + ++la G+kG+iSV++n+ lcl|NCBI__GCF_000092245.1:WP_013135926.1 144 DIEADTAIRLFDDIKnIYAIKEATGSLERAIELNAKR-ADFCVVSGDDLIDFPMLANGSKGIISVTANL 211 ***********99988*******************88.5****************************** PP TIGR00674 207 apkelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseek 275 +p+ +++vk + egd+e r i+++l l k++f+e NPip+K+a++++gl+ + e+RlPLt+ s e+ lcl|NCBI__GCF_000092245.1:WP_013135926.1 212 LPNYKSKLVKSVFEGDYETGRAINNELYALNKIMFCENNPIPIKAAMYIAGLMDTLEYRLPLTKPSLEN 280 ********************************************************************* PP TIGR00674 276 keklkevlke 285 +k++e++k+ lcl|NCBI__GCF_000092245.1:WP_013135926.1 281 MKKIEEIIKN 290 *******997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (295 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: 00:00:00.01 # Mc/sec: 7.27 // [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