Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_041313140.1 HM1_RS02480 shikimate dehydrogenase
Query= SwissProt::Q5KWX7 (276 letters) >NCBI__GCF_000019165.1:WP_041313140.1 Length = 299 Score = 213 bits (541), Expect = 5e-60 Identities = 120/279 (43%), Positives = 169/279 (60%), Gaps = 13/279 (4%) Query: 7 LIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVNVTIPHK 66 L+G+PV+HS SP MHN AF RLG+ RY +V+P +G A+AG+ ALG G NVT+PHK Sbjct: 19 LLGYPVKHSFSPAMHNAAFERLGLNWRYSAHAVKPEDLGKAVAGLAALGYRGANVTVPHK 78 Query: 67 LAVIPFLDEVDEHARRIGAVNTII-NNDGRLVGYNTDGLGYVQALEEEMNITLDGKRILV 125 V+ LD VD A+R+GAVNTI+ DG+ VGYNTDG+G++ L ++ + G L+ Sbjct: 79 EQVVSLLDRVDPSAKRLGAVNTIVMAGDGKTVGYNTDGIGFLHGLRQD-GFAVAGAAALL 137 Query: 126 IGAGGGARGIYFSLLSTAAERIDMANRTVEKAERLV--------REGDERRSAYFSLAEA 177 +G+GG AR + F+LL + + NRT EKAE L+ EG R+ + A Sbjct: 138 LGSGGAARAVAFALLDGGVRSLVVVNRTPEKAEALLDALRRSGAAEGAALRAGRWEEAFL 197 Query: 178 ETRLAEYDIIINTTSVGMHPRVE--VQPLSLER-LRPGVIVSDIIYNPLETKWLKEAKAR 234 E D+++N T+ GM PLS +R L PG V D++Y+P ET+ L A++ Sbjct: 198 RECAKEVDLVVNATASGMGKGEGSIAYPLSPKRWLSPGPFVCDLVYHPPETELLSVARSL 257 Query: 235 GARVQNGVGMLVYQGALAFEKWTGQWPDVNRMKQLVIEA 273 G R QNG+ ML++QGA AF WTGQ P + M + + +A Sbjct: 258 GCRCQNGLPMLLHQGAAAFALWTGQEPPLTVMAEALRQA 296 Lambda K H 0.320 0.138 0.400 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: 12 Number of successful extensions: 5 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: 276 Length of database: 299 Length adjustment: 26 Effective length of query: 250 Effective length of database: 273 Effective search space: 68250 Effective search space used: 68250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 bits)
Align candidate WP_041313140.1 HM1_RS02480 (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.20836.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-82 261.3 0.0 5.2e-82 261.0 0.0 1.0 1 lcl|NCBI__GCF_000019165.1:WP_041313140.1 HM1_RS02480 shikimate dehydrogen Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_041313140.1 HM1_RS02480 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.0 0.0 5.2e-82 5.2e-82 3 267 .. 17 295 .. 15 297 .. 0.88 Alignments for each domain: == domain 1 score: 261.0 bits; conditional E-value: 5.2e-82 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlell 71 ++++G+p+khS+sp++hnaa++ lgl+ +Y a+ v++e+l ka+ g+ alg +G+nvTvP+Ke+v++ll lcl|NCBI__GCF_000019165.1:WP_041313140.1 17 VALLGYPVKHSFSPAMHNAAFERLGLNWRYSAHAVKPEDLGKAVAGLAALGYRGANVTVPHKEQVVSLL 85 79******************************************************************* PP TIGR00507 72 DeieesakligavNTlk.ledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 D++++sak +gavNT++ dgk vgynTDgiG++ L++ + ++ +l++G GGaa+ava++Ll+ lcl|NCBI__GCF_000019165.1:WP_041313140.1 86 DRVDPSAKRLGAVNTIVmAGDGKTVGYNTDGIGFLHGLRQDGFAVAGAAALLLGSGGAARAVAFALLDG 154 ****************97789*******************888888**********************9 PP TIGR00507 140 .dkeviiaNRtvekaeelaerlqe.......lgeilalsleeve..lkkvdliinatsaglsgeid... 195 +++++NRt ekae+l+++l++ ++++ ++ k+vdl++nat++g+ + lcl|NCBI__GCF_000019165.1:WP_041313140.1 155 gVRSLVVVNRTPEKAEALLDALRRsgaaegaALRAGRWEEAFLRecAKEVDLVVNATASGMGKGEGsia 223 55789*******************6655333111223444333311466************76544221 PP TIGR00507 196 eaevkaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfea 264 + ++ l+ g +v+Dlvy+p et ll+ a+++g++ ++Gl Ml +Q+a +F lwtg+ep++ ++ ea lcl|NCBI__GCF_000019165.1:WP_041313140.1 224 YPLSPKRWLSPGPFVCDLVYHPPETELLSVARSLGCRCQNGLPMLLHQGAAAFALWTGQEPPLTVMAEA 292 4455677899**********************************************************9 PP TIGR00507 265 lke 267 l++ lcl|NCBI__GCF_000019165.1:WP_041313140.1 293 LRQ 295 986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.01 // [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