Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate WP_093396409.1 BM091_RS13075 4-hydroxy-tetrahydrodipicolinate synthase
Query= BRENDA::O67216 (294 letters) >NCBI__GCF_900114975.1:WP_093396409.1 Length = 292 Score = 318 bits (815), Expect = 9e-92 Identities = 157/291 (53%), Positives = 212/291 (72%), Gaps = 2/291 (0%) Query: 1 MFQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIE 60 MF+G+ VA++TPFK+G+VD +AL LI++ ++ GT I+ CGTTGES TL+FEEHE+V+E Sbjct: 1 MFKGAFVAIVTPFKDGKVDEDALRKLIDYQIEQGTHGIVPCGTTGESATLSFEEHERVVE 60 Query: 61 FAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKT 120 V+ R+ V+AGTG N T EA+ LT HA++VGADGAL++ PYYNKPTQ GLY HF+ Sbjct: 61 ITVEHVNKRVPVLAGTGSNNTAEAIRLTRHAEKVGADGALMISPYYNKPTQEGLYRHFEK 120 Query: 121 VAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGES 180 VA V+IPII+YNIP RT V I +TM +L S ENIV KE++ ++ ++ EI+ R GE+ Sbjct: 121 VAASVNIPIIVYNIPGRTAVNIEPETMERL-SRIENIVGVKEASGSIKQVMEIIARCGEN 179 Query: 181 FSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLF 240 F VLSG+D +T P+++LG KGVISV +NV PR++ ++ ALEG + AR +HY L L Sbjct: 180 FDVLSGEDYITFPLLSLGGKGVISVVSNVAPRDMADMCNFALEGKWDEARSLHYKLLPLC 239 Query: 241 KVLFIETNPIPVKTACWMLG-MCEKEFRLPLTEMSPENENKLREVLKKYNL 290 +LF ETNP+PVK A M+G + E RLPL +S N NKL+ VLK+Y L Sbjct: 240 NILFCETNPVPVKAALHMMGKIPSDEVRLPLAPLSENNRNKLQSVLKQYGL 290 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: 273 Number of extensions: 4 Number of successful extensions: 3 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 WP_093396409.1 BM091_RS13075 (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.2851039.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-126 405.0 0.0 7.3e-126 404.8 0.0 1.0 1 NCBI__GCF_900114975.1:WP_093396409.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900114975.1:WP_093396409.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 404.8 0.0 7.3e-126 7.3e-126 3 286 .] 6 288 .. 4 288 .. 0.99 Alignments for each domain: == domain 1 score: 404.8 bits; conditional E-value: 7.3e-126 TIGR00674 3 ltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGtg 75 +A++TPfk+ + vd +al kli++qie+g+ +iv++GtTGEsatLs+eE+++v+e++ve v++rvpv+aGtg NCBI__GCF_900114975.1:WP_093396409.1 6 FVAIVTPFKDGK-VDEDALRKLIDYQIEQGTHGIVPCGTTGESATLSFEEHERVVEITVEHVNKRVPVLAGTG 77 79******9988.************************************************************ PP TIGR00674 76 snateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepetvkrL 148 sn+t+eai+lt++aek+g+dg+l+++PyYnkPtqeGly+hf+++a++v++Pii+Yn+P+Rt+v++epet+ rL NCBI__GCF_900114975.1:WP_093396409.1 78 SNNTAEAIRLTRHAEKVGADGALMISPYYNKPTQEGLYRHFEKVAASVNIPIIVYNIPGRTAVNIEPETMERL 150 ************************************************************************* PP TIGR00674 149 aeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelkemvkaaleg 221 ++ ++iv++Keasg++++v+ei+a+ +e+f vlsG+D +t ++l+lG+kGviSV+snvap+++++m++ aleg NCBI__GCF_900114975.1:WP_093396409.1 151 SRIENIVGVKEASGSIKQVMEIIARCGENFDVLSGEDYITFPLLSLGGKGVISVVSNVAPRDMADMCNFALEG 223 ************************************************************************* PP TIGR00674 222 dteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklkevlkel 286 + +ear +h+kll+l+++lf+etNP+pvK+al+++g i +de+RlPL++lse++++kl++vlk++ NCBI__GCF_900114975.1:WP_093396409.1 224 KWDEARSLHYKLLPLCNILFCETNPVPVKAALHMMGKIPSDEVRLPLAPLSENNRNKLQSVLKQY 288 **************************************************************985 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.99 // [ok]
This GapMind analysis is from Jul 25 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