Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate AZOBR_RS27060 AZOBR_RS27060 dihydrodipicolinate synthase (DapA)
Query= SwissProt::Q57695 (289 letters) >FitnessBrowser__azobra:AZOBR_RS27060 Length = 299 Score = 161 bits (407), Expect = 2e-44 Identities = 97/284 (34%), Positives = 163/284 (57%), Gaps = 5/284 (1%) Query: 4 GVYPAIITPFK-NKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEKV 62 G++ AI+TP + VD GL+ + ++ G SG+V +G TGE P LS +E K+V+ Sbjct: 10 GLFSAIVTPLTVDGSVDIAGLKRLVRHQLDAGASGVVPIGGTGEYPALSRDERKRVVAAC 69 Query: 63 VDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGKVA 122 V+ G+ VI G S ++A+E GA AV+++TPYY TQEG+R +F Sbjct: 70 VEEAGGK-PVIPGVLSTGFQDAVEAGRDFAAAGAAAVMTVTPYYAAGTQEGMRAYFRAYR 128 Query: 123 ESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDA--KIT 180 ++++LP++LY +P RT V + + V+ +AE+ S I +K ++ ++ + + + A KI+ Sbjct: 129 DAVDLPVMLYQIPRRTTVAVTAEGVQAMAEDGS-IIGMKFSSYDMPEFIKTMKYAGDKIS 187 Query: 181 VLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLMKA 240 VLSG + L +ALG +G + A I PK ++ + A G +A ++ P++ + Sbjct: 188 VLSGEEPLFATHVALGARGGVLASATIYPKIWLRIFALARAGKLNEALAEQTQIDPVVNS 247 Query: 241 MFIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLK 284 +F+ETNP P+K + M G P G +RLPL + E + L+ V + Sbjct: 248 IFLETNPGPLKAFMAMAGMPVGGVRLPLTAPTAETTEKLQAVAR 291 Lambda K H 0.315 0.135 0.374 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: 196 Number of extensions: 8 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: 289 Length of database: 299 Length adjustment: 26 Effective length of query: 263 Effective length of database: 273 Effective search space: 71799 Effective search space used: 71799 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 48 (23.1 bits)
Align candidate AZOBR_RS27060 AZOBR_RS27060 (dihydrodipicolinate synthase (DapA))
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.3669.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-70 222.6 0.0 2.8e-70 222.4 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS27060 AZOBR_RS27060 dihydrodipicolinat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS27060 AZOBR_RS27060 dihydrodipicolinate synthase (DapA) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 222.4 0.0 2.8e-70 2.8e-70 2 285 .. 11 292 .. 10 293 .. 0.99 Alignments for each domain: == domain 1 score: 222.4 bits; conditional E-value: 2.8e-70 TIGR00674 2 vltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpv 70 + +A++TP+ dgsvd+a l++l+++q+++g +++v++G TGE ++Ls +E+k+v+ ve + + pv lcl|FitnessBrowser__azobra:AZOBR_RS27060 11 LFSAIVTPLTVDGSVDIAGLKRLVRHQLDAGASGVVPIGGTGEYPALSRDERKRVVAACVEEAGG-KPV 78 679************************************************************99.9** PP TIGR00674 71 iaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvs 139 i G+ s+ ++a+e + ++ +g+++v++vtPyY tqeG+ ++f a ++v+lP++lY++P Rt+v lcl|FitnessBrowser__azobra:AZOBR_RS27060 79 IPGVLSTGFQDAVEAGRDFAAAGAAAVMTVTPYYAAGTQEGMRAYFRAYRDAVDLPVMLYQIPRRTTVA 147 ********************************************************************* PP TIGR00674 140 lepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvap 208 ++ e v+++ae+ +i+++K +s d+ ++ + +++a+++++vlsG++ l +alGa+G + + + p lcl|FitnessBrowser__azobra:AZOBR_RS27060 148 VTAEGVQAMAEDGSIIGMKFSSYDMPEFIKTMKYAGDKISVLSGEEPLFATHVALGARGGVLASATIYP 216 ********************************************************************* PP TIGR00674 209 kelkemvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekke 277 k + + a +g+ +ea+ ++++ ++++ +f+etNP p+K+ +a++g++++ +RlPLt+ + e++e lcl|FitnessBrowser__azobra:AZOBR_RS27060 217 KIWLRIFALARAGKLNEALAEQTQIDPVVNSIFLETNPGPLKAFMAMAGMPVG-GVRLPLTAPTAETTE 284 *****************************************************.*************** PP TIGR00674 278 klkevlke 285 kl++v ++ lcl|FitnessBrowser__azobra:AZOBR_RS27060 285 KLQAVARH 292 ***99765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (299 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.94 // [ok]
This GapMind analysis is from Apr 09 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