Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_041456249.1 AVA_RS15705 shikimate dehydrogenase
Query= SwissProt::Q58484 (282 letters) >NCBI__GCF_000204075.1:WP_041456249.1 Length = 293 Score = 180 bits (456), Expect = 4e-50 Identities = 116/288 (40%), Positives = 163/288 (56%), Gaps = 18/288 (6%) Query: 1 MINAKTKVIGLIGHPVEHSFSPIMHNAAFKDKGLNYVYVAFDVLPENLKYVIDGAKALGI 60 MI KTK++G+IGHPVEHS SP+MHNAA GL+YVY+ F + P+NL+ I +G+ Sbjct: 5 MITGKTKLLGVIGHPVEHSLSPVMHNAAIAQLGLDYVYLPFPIAPDNLEAAIALLATIGV 64 Query: 61 VGFNVTIPHKIEIMKYLDEIDKDAQLIGAVNTIKIEDGKAIGYNTDGIGARMALEEEIGR 120 VGF+VTIPHK I+ L EI AQ IGAVNT+ ++ + +G NTD G L+ R Sbjct: 65 VGFSVTIPHKQAIIPLLAEISPVAQAIGAVNTVTRQNNQWVGTNTDIEGFIAPLQTTYKR 124 Query: 121 VKDKNI-VIYGAGGAARAV---AFELAKDNNIIIANRTVEKAEALA-----KEIAEKLNK 171 + I VI G GGAARAV ++L I + R V++ E IAE L Sbjct: 125 DWSQQIAVILGNGGAARAVVAGCYQLG-FAEIHVVGRNVQRLEEFRHSWDNSPIAENL-- 181 Query: 172 KFGEEVKFSGLDVDLDGVDIIINATPIGMYPNIDVEPIVKAE--KLREDMVVMDLIYNPL 229 + + L + ++++N TPIGMYP +D P+ E L+ + DLIY P Sbjct: 182 ---QVHTWDYLAKLVPQANLLVNTTPIGMYPQVDESPLSTEELANLQTGAIAYDLIYIPK 238 Query: 230 ETVLLKEAKKVNAKTINGLGMLIYQGAVAFKIWTGVEP-NIEVMKNAI 276 T L++A++ A I+GL ML+ QG A KIW + ++VM+ A+ Sbjct: 239 PTQFLQKAQQQGAIAIDGLEMLVQQGVAALKIWLQQDDIPVDVMRQAL 286 Lambda K H 0.318 0.139 0.385 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: 4 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: 282 Length of database: 293 Length adjustment: 26 Effective length of query: 256 Effective length of database: 267 Effective search space: 68352 Effective search space used: 68352 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: 41 (21.6 bits) S2: 47 (22.7 bits)
Align candidate WP_041456249.1 AVA_RS15705 (shikimate dehydrogenase)
to HMM TIGR00507 (aroE: shikimate dehydrogenase (EC 1.1.1.25))
# 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/TIGR00507.hmm # target sequence database: /tmp/gapView.30232.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00507 [M=270] Accession: TIGR00507 Description: aroE: shikimate dehydrogenase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-70 221.5 0.0 6.5e-70 221.3 0.0 1.0 1 lcl|NCBI__GCF_000204075.1:WP_041456249.1 AVA_RS15705 shikimate dehydrogen Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_041456249.1 AVA_RS15705 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 221.3 0.0 6.5e-70 6.5e-70 1 269 [. 11 290 .. 11 291 .. 0.91 Alignments for each domain: == domain 1 score: 221.3 bits; conditional E-value: 6.5e-70 TIGR00507 1 kllgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevle 69 kllgviG+p++hS+sp++hnaa++qlgl+++Yl f++ +++le a+ + + g+ G++vT+P+K+++++ lcl|NCBI__GCF_000204075.1:WP_041456249.1 11 KLLGVIGHPVEHSLSPVMHNAAIAQLGLDYVYLPFPIAPDNLEAAIALLATIGVVGFSVTIPHKQAIIP 79 689****************************************************************** PP TIGR00507 70 llDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLl 137 ll ei++ a++igavNT+++++++ vg nTD +G+++ L+ ++ s++ ++i+G GGaa+av+ lcl|NCBI__GCF_000204075.1:WP_041456249.1 80 LLAEISPVAQAIGAVNTVTRQNNQWVGTNTDIEGFIAPLQTtYKRDWSQQIAVILGNGGAARAVVAGCY 148 *****************************************87777889999****************9 PP TIGR00507 138 ka.dkeviiaNRtvekaeelaerlqe.....lgeilalsleevelkkvdliinatsaglsgeideaevk 200 + e+ ++ R v++ ee + + + ++ +++ + +l++n+t++g+++++de +++ lcl|NCBI__GCF_000204075.1:WP_041456249.1 149 QLgFAEIHVVGRNVQRLEEFRHSWDNspiaeNLQVHTWDYLAKLVPQANLLVNTTPIGMYPQVDESPLS 217 995589************999888776753344455555555555679********************9 PP TIGR00507 201 ael...lkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgve.pdvekvfeal 265 +e l++g++++Dl+y+p+ t +l+ a+++g+ idGl+Mlv+Q++ + ++w + ++v+++++al lcl|NCBI__GCF_000204075.1:WP_041456249.1 218 TEElanLQTGAIAYDLIYIPKPTQFLQKAQQQGAIAIDGLEMLVQQGVAALKIWLQQDdIPVDVMRQAL 286 98622256899*******************************************999889********9 PP TIGR00507 266 kekl 269 +++l lcl|NCBI__GCF_000204075.1:WP_041456249.1 287 QKHL 290 9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (293 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 8.32 // [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