Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_012972230.1 ALVIN_RS15290 shikimate dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_000025485.1:WP_012972230.1 Length = 281 Score = 297 bits (760), Expect = 2e-85 Identities = 162/271 (59%), Positives = 192/271 (70%), Gaps = 5/271 (1%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGG-NVT 60 D Y V G+PI HSKSP+IH FA QTGQDLEY LL LD+F+ R F + G G NVT Sbjct: 3 DHYAVIGHPIAHSKSPVIHAAFARQTGQDLEYGRLLGALDDFAGDVRRFLESGGLGLNVT 62 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFKE+A+ L D + RA AGAVNTL +L DG L+G+NTDG GLVRDLT N G + AG Sbjct: 63 VPFKEQAWALADERSARAELAGAVNTLIRLDDGRLRGENTDGVGLVRDLTDNHGFDFAGA 122 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQ-E 179 R+L+LGAGGA RGVL+P+L LVIANRT KA +LAR LGPV GF L E Sbjct: 123 RVLMLGAGGAARGVLQPLLGTGLARLVIANRTASKALELARLGRALGPVEGCGFDGLAGE 182 Query: 180 PVDVIINATSASLAGELPPIADS-LVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDG 238 D+II+ATSA LA +P I D L G T YDM+YG PTPFC+W ++ GAA+VLDG Sbjct: 183 RFDLIIHATSAGLADAVPAIPDDCLAPDGWT--YDMLYGDRPTPFCRWGSEHGAARVLDG 240 Query: 239 LGMLAEQAAEAFFIWRGVRPDTAPVLAELRR 269 LGML EQAAE+F++WRGVRP+T PV+A LRR Sbjct: 241 LGMLIEQAAESFWLWRGVRPETGPVIASLRR 271 Lambda K H 0.319 0.137 0.405 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: 290 Number of extensions: 11 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: 274 Length of database: 281 Length adjustment: 25 Effective length of query: 249 Effective length of database: 256 Effective search space: 63744 Effective search space used: 63744 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_012972230.1 ALVIN_RS15290 (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.13274.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-80 256.5 0.0 1.5e-80 256.2 0.0 1.0 1 lcl|NCBI__GCF_000025485.1:WP_012972230.1 ALVIN_RS15290 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025485.1:WP_012972230.1 ALVIN_RS15290 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.2 0.0 1.5e-80 1.5e-80 2 265 .. 4 269 .. 3 273 .. 0.97 Alignments for each domain: == domain 1 score: 256.2 bits; conditional E-value: 1.5e-80 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++viG+pi+hSksp+ih a+++q+g++leY ++ ++++ + + + g G+nvTvPfKe++ +l lcl|NCBI__GCF_000025485.1:WP_012972230.1 4 HYAVIGHPIAHSKSPVIHAAFARQTGQDLEYGRLLGALDDFAGDVRRFLESGGLGLNVTVPFKEQAWAL 72 69******************************************************************* PP TIGR00507 71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLl 137 +De + +a+l+gavNTl l+dg+l g+nTDg+Glv +L + ++ rvl++GAGGaa++v+ +Ll lcl|NCBI__GCF_000025485.1:WP_012972230.1 73 ADERSARAELAGAVNTLIrLDDGRLRGENTDGVGLVRDLTDnHGFDFAGARVLMLGAGGAARGVLQPLL 141 ****************988*********************977777789******************** PP TIGR00507 138 ka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellk 205 + +++iaNRt +ka ela ++lg + + + +++dlii+atsagl + ++++ + l+ lcl|NCBI__GCF_000025485.1:WP_012972230.1 142 GTgLARLVIANRTASKALELARLGRALGPVEGCGFDGLAGERFDLIIHATSAGLADAV--PAIPDDCLA 208 994468****************************************************..********* PP TIGR00507 206 egklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 + +D+ y tp+ ++ +++g ++v+dGlgMl++Qaa sF lw+gv p+ v+ l lcl|NCBI__GCF_000025485.1:WP_012972230.1 209 PDGWTYDMLYGDRPTPFCRWGSEHGaARVLDGLGMLIEQAAESFWLWRGVRPETGPVIASL 269 *************************99**************************99988766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (281 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.29 // [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