Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_028315051.1 G491_RS0114125 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::Q9I4W3 (292 letters) >NCBI__GCF_000429905.1:WP_028315051.1 Length = 344 Score = 189 bits (479), Expect = 1e-52 Identities = 120/294 (40%), Positives = 169/294 (57%), Gaps = 21/294 (7%) Query: 1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60 M G ALVTPF ++G LD L KLV+F + G + I+AVGTTGES TL EEH+QVI Sbjct: 1 MTKGCNTALVTPF-SEGGLDITGLEKLVEFQIAGGVDGILAVGTTGESPTLSWEEHLQVI 59 Query: 61 RRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQ-EGMYQHF 119 + V D+ KG++ IAGTG+N+T+E + T+ A G DA LLV PYYN P+ E ++ Sbjct: 60 QIVADKTKGKVKCIAGTGSNNTKETLEATKHAAKAGVDAVLLVDPYYNGPSSLEIRREYL 119 Query: 120 RHIAEAVAIPQIL-YNVPGRTSCDMLPETVERLSK-VPNIIGIKEATGDLQRAKEVIERV 177 A+A +I+ Y +PGRT + PE + L K PN+ +KEATGDL ++ + Sbjct: 120 TPTAKAFPDLEIIPYVIPGRTGAQLFPEDLAILYKECPNVKTVKEATGDLDNMRKTRKLC 179 Query: 178 GKDFLVYSGDDATAVELML---LGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAIND 234 G D+ + SGDD +++ML + G ISV +NVAP+A+S + AAA GDA AR I Sbjct: 180 GPDYTIMSGDDDMTLQMMLDPDIKASGVISVLSNVAPKAVSQMTAAAAAGDADLARNIGA 239 Query: 235 RLMPLHKALFIES--------------NPIPVKWALHEMGLIPEGIRLPLTWLS 274 L PL + +++ NP+ VK + +G+ R PL +S Sbjct: 240 ALKPLFGLVVVKTTEESPVGPVMCRARNPLGVKTLMAALGMPCGPCRPPLGKMS 293 Lambda K H 0.319 0.134 0.393 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: 225 Number of extensions: 8 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: 292 Length of database: 344 Length adjustment: 27 Effective length of query: 265 Effective length of database: 317 Effective search space: 84005 Effective search space used: 84005 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_028315051.1 G491_RS0114125 (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.9220.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-76 241.2 0.1 2.9e-75 238.8 0.1 1.8 1 lcl|NCBI__GCF_000429905.1:WP_028315051.1 G491_RS0114125 4-hydroxy-tetrahy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_028315051.1 G491_RS0114125 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 238.8 0.1 2.9e-75 2.9e-75 3 281 .. 6 302 .. 4 307 .. 0.92 Alignments for each domain: == domain 1 score: 238.8 bits; conditional E-value: 2.9e-75 TIGR00674 3 ltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpvi 71 tAl+TPf e g +d++ lekl+e+qi+ gvd+i++vGtTGEs+tLs+eE+ +vi+++++ +k++v+ i lcl|NCBI__GCF_000429905.1:WP_028315051.1 6 NTALVTPFSEGG-LDITGLEKLVEFQIAGGVDGILAVGTTGESPTLSWEEHLQVIQIVADKTKGKVKCI 73 69*******999.******************************************************** PP TIGR00674 72 aGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfka.iaeev.elPiilYnvPsRtgv 138 aGtgsn+t+e++e tk+a+k+gvd+vl+v PyYn P+ + + + + a++ +l ii Y +P+Rtg+ lcl|NCBI__GCF_000429905.1:WP_028315051.1 74 AGTGSNNTKETLEATKHAAKAGVDAVLLVDPYYNGPSSLEIRREYLTpTAKAFpDLEIIPYVIPGRTGA 142 ************************************9888877665515555579************** PP TIGR00674 139 slepetvkrLaeeve.ivaiKeasgdlervseikaeakedfkvlsGdDaltleila...lGakGviSVa 203 +l pe ++ L +e++ + ++Kea+gdl+++ + ++ + d++++sGdD +tl++++ + a+GviSV+ lcl|NCBI__GCF_000429905.1:WP_028315051.1 143 QLFPEDLAILYKECPnVKTVKEATGDLDNMRKTRKLCGPDYTIMSGDDDMTLQMMLdpdIKASGVISVL 211 ************9998***************************************744468******** PP TIGR00674 204 snvapkelkemvkaalegdteeareihqkllklfkalfiet..............NPipvKtalallgl 258 snvapk +++m +aa++gd + ar+i + l++lf + ++t NP++vKt++a+lg+ lcl|NCBI__GCF_000429905.1:WP_028315051.1 212 SNVAPKAVSQMTAAAAAGDADLARNIGAALKPLFGLVVVKTteespvgpvmcrarNPLGVKTLMAALGM 280 *********************************9988876556666666666666************** PP TIGR00674 259 iekdelRlPLtelseekkeklke 281 + + +R+PL ++s++ + + + lcl|NCBI__GCF_000429905.1:WP_028315051.1 281 PCG-PCRPPLGKMSKQGLDVVVN 302 ***.9*********998777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (344 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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 2.95 // [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