Align dihydrodipicolinate synthase subunit (EC 4.3.3.7) (characterized)
to candidate WP_015944705.1 DHAF_RS18260 4-hydroxy-tetrahydrodipicolinate synthase
Query= metacyc::MONOMER-6565 (289 letters) >NCBI__GCF_000021925.1:WP_015944705.1 Length = 291 Score = 296 bits (758), Expect = 4e-85 Identities = 142/285 (49%), Positives = 197/285 (69%) Query: 1 MNFGNIATAMVTPFDKNENIDFQKLSKLIDYLLNNGTDSLVVAGTTGESPTLSEEEKVAL 60 M I TAMVTPF+ +++ + KL +YL+ +G D +VV GTTGESPT+S EEK+ L Sbjct: 1 MALNRIMTAMVTPFNDKMEVNYPEAEKLANYLIEHGNDGIVVCGTTGESPTVSAEEKIEL 60 Query: 61 IQYSVKEAAGRAPIIAGTGSNNTKASIKLTKKAEEAGADAVMLVTPYYNKPSQEGMYRHF 120 + K RA +IAG GSN T SI L ++AE+ G D +M V PYYNKPSQEG+Y+HF Sbjct: 61 FKTVKKAVGSRATVIAGIGSNTTDGSINLARQAEKTGVDGLMAVVPYYNKPSQEGLYQHF 120 Query: 121 RAIAEETSLPVMLYNVPGRTAASLAPETTIRLAEIPNIIAIKEASGDLDAITKIVAETPE 180 RAIAE SLP+M+YN+PGRT+ +L PET +RL+EIPNI +IKEA+G +D ++++ PE Sbjct: 121 RAIAEAISLPLMVYNIPGRTSINLLPETVLRLSEIPNITSIKEAAGSMDQVSEMRRILPE 180 Query: 181 DFAVYSGDDSLTLPALSVGARGIVSVASHIIGPEMQEMIKHYTEGNTAQAALIHQKLLPL 240 DF +YSGDDSLTLP LS+G GI+SVA+H++G E+++++ + G A H KL+P+ Sbjct: 181 DFLIYSGDDSLTLPMLSLGCDGIISVAAHVVGDEIKQLVDAWFNGEPQTALQWHLKLMPM 240 Query: 241 MKGLFAAPNPSPLKTALQLKGLDVGSVRLPLIPLNEDERLRLSSL 285 KG+F NP P+K L+ G++ G V+LPL+ +E L L Sbjct: 241 FKGVFVTTNPVPVKYLLKKAGINAGGVKLPLVCAAPEEEAFLDDL 285 Lambda K H 0.313 0.131 0.357 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: 272 Number of extensions: 5 Number of successful extensions: 1 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: 289 Length of database: 291 Length adjustment: 26 Effective length of query: 263 Effective length of database: 265 Effective search space: 69695 Effective search space used: 69695 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_015944705.1 DHAF_RS18260 (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.7781.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-109 348.6 0.0 1.1e-108 348.4 0.0 1.0 1 lcl|NCBI__GCF_000021925.1:WP_015944705.1 DHAF_RS18260 4-hydroxy-tetrahydr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021925.1:WP_015944705.1 DHAF_RS18260 4-hydroxy-tetrahydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 348.4 0.0 1.1e-108 1.1e-108 2 283 .. 6 286 .. 5 289 .. 0.98 Alignments for each domain: == domain 1 score: 348.4 bits; conditional E-value: 1.1e-108 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 ++tA++TPf+++ +v + ekl +++ie+g d+ivv+GtTGEs+t s eEk+++++++ + v r v lcl|NCBI__GCF_000021925.1:WP_015944705.1 6 IMTAMVTPFNDKMEVNYPEAEKLANYLIEHGNDGIVVCGTTGESPTVSAEEKIELFKTVKKAVGSRATV 74 689****************************************************************** PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 iaG+gsn+t+ +i+l+++aek+gvdg+++v+PyYnkP+qeGly+hf aiae+++lP+++Yn+P+Rt+++ lcl|NCBI__GCF_000021925.1:WP_015944705.1 75 IAGIGSNTTDGSINLARQAEKTGVDGLMAVVPYYNKPSQEGLYQHFRAIAEAISLPLMVYNIPGRTSIN 143 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvap 208 l petv+rL+e ++i++iKea+g++++vse++++ +edf ++sGdD+ltl++l+lG G+iSVa++v++ lcl|NCBI__GCF_000021925.1:WP_015944705.1 144 LLPETVLRLSEIPNITSIKEAAGSMDQVSEMRRILPEDFLIYSGDDSLTLPMLSLGCDGIISVAAHVVG 212 ********************************************************************* PP TIGR00674 209 kelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekke 277 +e+k++v a+ +g+ + a++ h kl+++fk +f++tNP+pvK++l+ +g+ ++ ++lPL+ + e++ lcl|NCBI__GCF_000021925.1:WP_015944705.1 213 DEIKQLVDAWFNGEPQTALQWHLKLMPMFKGVFVTTNPVPVKYLLKKAGINAG-GVKLPLVCAAPEEEA 280 *****************************************************.**********99998 PP TIGR00674 278 klkevl 283 l++ lcl|NCBI__GCF_000021925.1:WP_015944705.1 281 FLDDLY 286 888765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (291 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.08 // [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