Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate RR42_RS04230 RR42_RS04230 dihydrodipicolinate synthase
Query= SwissProt::Q57695 (289 letters) >FitnessBrowser__Cup4G11:RR42_RS04230 Length = 302 Score = 149 bits (377), Expect = 6e-41 Identities = 90/288 (31%), Positives = 145/288 (50%), Gaps = 2/288 (0%) Query: 2 FKGVYPAIITPFKNKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEK 61 F G++ ++TPF + VDF L + +G++GIV G+TGE+ L E V++ Sbjct: 11 FSGIWLPLVTPFADGSVDFPALARLVAHYAGSGIAGIVVCGSTGEAAALDEAEQLAVLDT 70 Query: 62 VVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGKV 121 V+ ++ AGS + + A + +L+ PYY +P+Q GL +F + Sbjct: 71 VLASAGSLPVMMGVAGSQVKQVQARVRRLA-GLPLAGLLAPAPYYVRPSQAGLLDYFRTL 129 Query: 122 AESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAKITV 181 A+S P+VLY++P RT V LE +T+ LA + NI A+K+ + +I DA+++V Sbjct: 130 ADSAAAPLVLYDIPYRTGVKLETETILALAA-HPNIRAIKDCGGDYHGTQAVIADARLSV 188 Query: 182 LSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLMKAM 241 L+G D L + LGG G I A++ P FV + E AR + + + P++K + Sbjct: 189 LAGEDHQLLGTLCLGGAGAIIASAHLYPALFVALAQAVAGQRLEHARRLFHAVMPVIKLL 248 Query: 242 FIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLKDLGLI 289 F E NP P+K L G ELR P+ + L + LG + Sbjct: 249 FAEPNPGPLKAMLAREGWTRNELRAPMKSAGAALEAALAQACERLGAV 296 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: 209 Number of extensions: 7 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: 302 Length adjustment: 26 Effective length of query: 263 Effective length of database: 276 Effective search space: 72588 Effective search space used: 72588 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 RR42_RS04230 RR42_RS04230 (dihydrodipicolinate 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.22832.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-68 216.2 0.0 2.3e-68 216.1 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS04230 RR42_RS04230 dihydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS04230 RR42_RS04230 dihydrodipicolinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.1 0.0 2.3e-68 2.3e-68 6 280 .. 18 287 .. 13 293 .. 0.96 Alignments for each domain: == domain 1 score: 216.1 bits; conditional E-value: 2.3e-68 TIGR00674 6 liTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelvknrvpviaGt 74 l+TPf + svdf al++l+ + +g+ +ivv+G+TGE+a+L E+ +v+ +++ + +pv+ G+ lcl|FitnessBrowser__Cup4G11:RR42_RS04230 18 LVTPFADG-SVDFPALARLVAHYAGSGIAGIVVCGSTGEAAALDEAEQLAVLDTVLASAGS-LPVMMGV 84 8****865.5*********************************************999887.******* PP TIGR00674 75 gsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelPiilYnvPsRtgvslepe 143 ++ +++++ +++++ l+ +g+l+ +PyY++P+q Gl+ +f ++a+++ P++lY++P Rtgv+le e lcl|FitnessBrowser__Cup4G11:RR42_RS04230 85 AGSQVKQVQARVRRLAGLPLAGLLAPAPYYVRPSQAGLLDYFRTLADSAAAPLVLYDIPYRTGVKLETE 153 ********************************************************************* PP TIGR00674 144 tvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDaltleilalGakGviSVasnvapkelk 212 t+++La++++i aiK+++gd + + ++a a ++vl+G+D+ l l+lG++G i +++ p ++ lcl|FitnessBrowser__Cup4G11:RR42_RS04230 154 TILALAAHPNIRAIKDCGGDYHGTQAVIADA--RLSVLAGEDHQLLGTLCLGGAGAIIASAHLYPALFV 220 ***************************9976..5*********************************** PP TIGR00674 213 emvkaalegdteeareihqkllklfkalfietNPipvKtalallgliekdelRlPLtelseekkeklk 280 + +a++ ++ e+ar + + ++++k lf e+NP p+K++la +g++ + elR P+ + + l+ lcl|FitnessBrowser__Cup4G11:RR42_RS04230 221 ALAQAVAGQRLEHARRLFHAVMPVIKLLFAEPNPGPLKAMLAREGWTRN-ELRAPMKSAGAALEAALA 287 *************************************************.******988776666665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (302 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: 00:00:00.01 # Mc/sec: 8.28 // [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