Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate Ac3H11_1501 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= SwissProt::Q57695 (289 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1501 Length = 309 Score = 148 bits (373), Expect = 2e-40 Identities = 90/272 (33%), Positives = 143/272 (52%), Gaps = 2/272 (0%) Query: 2 FKGVYPAIITPFKNKEVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIEK 61 F G++ A++TPFK+ VD L L GV+G VA G+TGE+ L E +V+E Sbjct: 23 FSGLWIALVTPFKDGAVDHPALAALTARLRAQGVAGFVACGSTGEAAALDKAEQLQVLET 82 Query: 62 VVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGKV 121 V+ G V+ +G + + ++ A A ++S P+Y +P+QEGL F + Sbjct: 83 VLQAAQGLPVVMGVSGYHQGQVLQQVQALARYPVAGLLVS-APHYIRPSQEGLLHWFRTL 141 Query: 122 AESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAKITV 181 A++ +P+++Y++P RT + +T+ LA + I A+K+ + ++ LI D ++ V Sbjct: 142 ADASAVPLLIYDIPYRTGATITTETLLALAA-HPRIQAIKDCGGSPAKTQALISDGRLQV 200 Query: 182 LSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFPLMKAM 241 L+G D +ALGG G IS A+ FVE++ GD +AR + L P ++ Sbjct: 201 LTGEDAQIFHTLALGGAGAISASAHWQTPRFVELMALLRAGDLGEARRVWRALLPWIEVC 260 Query: 242 FIETNPIPVKTALNMMGRPAGELRLPLCEMSE 273 F E NP P+KT L G ELR P+ SE Sbjct: 261 FAEPNPAPLKTVLAHAGEMCNELRAPMMGASE 292 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: 203 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: 309 Length adjustment: 27 Effective length of query: 262 Effective length of database: 282 Effective search space: 73884 Effective search space used: 73884 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 Ac3H11_1501 (4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))
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.31150.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-68 215.6 0.0 4e-68 215.3 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 4-hydroxy-tetrahydrodipicolinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 215.3 0.0 4e-68 4e-68 3 277 .. 27 296 .. 25 302 .. 0.97 Alignments for each domain: == domain 1 score: 215.3 bits; conditional E-value: 4e-68 TIGR00674 3 ltAliTPfkedgsvdfaalekliesqiekgvdaivvvGtTGEsatLsleEkkkvievavelv 64 Al+TPfk+ vd al+ l ++ ++gv + v++G+TGE+a+L + E+ +v+e++++ + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 27 WIALVTPFKDGA-VDHPALAALTARLRAQGVAGFVACGSTGEAAALDKAEQLQVLETVLQAA 87 679*****9888.************************************************* PP TIGR00674 65 knrvpviaGtgsnateeaieltkeaeklgvdgvlvvtPyYnkPtqeGlykhfkaiaeevelP 126 ++ +pv+ G+++ ++++ ++ ++ +v+g+lv++P Y +P+qeGl+++f ++a+++ +P lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 88 QG-LPVVMGVSGYHQGQVLQQVQALARYPVAGLLVSAPHYIRPSQEGLLHWFRTLADASAVP 148 *9.*********************************************************** PP TIGR00674 127 iilYnvPsRtgvslepetvkrLaeeveivaiKeasgdlervseikaeakedfkvlsGdDalt 188 +++Y++P Rtg+ ++ et+++La++++i aiK+++g+ ++ + +++ + ++vl+G+Da lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 149 LLIYDIPYRTGATITTETLLALAAHPRIQAIKDCGGSPAKTQALIS--DGRLQVLTGEDAQI 208 *******************************************999..557*********** PP TIGR00674 189 leilalGakGviSVasnvapkelkemvkaalegdteeareihqkllklfkalfietNPipvK 250 + lalG++G iS ++ + ++ e+++ +gd ear + + ll+ +++ f e+NP p+K lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 209 FHTLALGGAGAISASAHWQTPRFVELMALLRAGDLGEARRVWRALLPWIEVCFAEPNPAPLK 270 ************************************************************** PP TIGR00674 251 talallgliekdelRlPLtelseekke 277 t+la +g + + elR P++ +se + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1501 271 TVLAHAGEMCN-ELRAPMMGASEALNL 296 *******9999.*******99987665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (286 nodes) Target sequences: 1 (309 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: 00:00:00.01 # Mc/sec: 8.80 // [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