Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_046007531.1 OLEAN_RS00125 shikimate dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_000967895.1:WP_046007531.1 Length = 279 Score = 331 bits (848), Expect = 1e-95 Identities = 162/270 (60%), Positives = 202/270 (74%), Gaps = 1/270 (0%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGGNVTV 61 D Y V GNPI HSKSP IH FAEQTGQDL Y+ +L PL++F + A FF+ G G NVTV Sbjct: 3 DLYAVMGNPINHSKSPQIHSAFAEQTGQDLIYSAILVPLEKFKEEANSFFRNGLGLNVTV 62 Query: 62 PFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGKR 121 PFKE+A++ D+ + RA RAGAVNTL K DG++ DNTDG G+VRD+T+N +AGKR Sbjct: 63 PFKEDAWQYADTYSSRALRAGAVNTLIKKEDGSIHADNTDGIGMVRDITINHDCAIAGKR 122 Query: 122 ILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQEPV 181 +L+LGAGGAVRG+LEP+L KP +V+ANRTV KA+ LA +F ++G +V GF ++ P Sbjct: 123 VLVLGAGGAVRGILEPVLEEKPLEVVVANRTVSKAQALAIDFSDIGKIVGCGFDQIEGPF 182 Query: 182 DVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGLGM 241 D+IIN TSASL+GELPPI S++ A T CYDMMYG EPT F QWA L AA LDGLGM Sbjct: 183 DLIINGTSASLSGELPPIPTSVIHA-ETTCYDMMYGAEPTVFNQWAESLNAAATLDGLGM 241 Query: 242 LAEQAAEAFFIWRGVRPDTAPVLAELRRQL 271 L EQAAE+F WRGVRP++APV++ +R L Sbjct: 242 LVEQAAESFNAWRGVRPESAPVISRIRDSL 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: 271 Number of extensions: 5 Number of successful extensions: 2 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: 279 Length adjustment: 25 Effective length of query: 249 Effective length of database: 254 Effective search space: 63246 Effective search space used: 63246 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_046007531.1 OLEAN_RS00125 (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.9066.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-81 258.9 0.0 2.5e-81 258.8 0.0 1.0 1 lcl|NCBI__GCF_000967895.1:WP_046007531.1 OLEAN_RS00125 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000967895.1:WP_046007531.1 OLEAN_RS00125 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.8 0.0 2.5e-81 2.5e-81 2 269 .. 4 271 .. 3 272 .. 0.96 Alignments for each domain: == domain 1 score: 258.8 bits; conditional E-value: 2.5e-81 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 l++v+Gnpi+hSksp ih a+++q+g++l Y a+ v++e++++ + ++ +gl G+nvTvPfKe + ++ lcl|NCBI__GCF_000967895.1:WP_046007531.1 4 LYAVMGNPINHSKSPQIHSAFAEQTGQDLIYSAILVPLEKFKEEANSFFRNGL-GLNVTVPFKEDAWQY 71 89*************************************************96.*************** PP TIGR00507 71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLl 137 +D ++ +a +gavNTl edg + ++nTDgiG+v ++ + ++krvl++GAGGa ++++ + l lcl|NCBI__GCF_000967895.1:WP_046007531.1 72 ADTYSSRALRAGAVNTLIkKEDGSIHADNTDGIGMVRDITInHDCAIAGKRVLVLGAGGAVRGILEPVL 140 ****************9779*******************987888899*****************9987 PP TIGR00507 138 ka.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellk 205 ++ + ev++aNRtv+ka++la + +g+i+ +++e +dliin tsa+lsge+ +++++++++ lcl|NCBI__GCF_000967895.1:WP_046007531.1 141 EEkPLEVVVANRTVSKAQALAIDFSDIGKIVGCGFDQIEG-PFDLIINGTSASLSGEL--PPIPTSVIH 206 7659******************************999986.5****************..********* PP TIGR00507 206 egklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 +++ ++D++y t++ ++a++++ + ++dGlgMlv+Qaa sF+ w+gv p+ v++++++ l lcl|NCBI__GCF_000967895.1:WP_046007531.1 207 AETTCYDMMYGAEPTVFNQWAESLNaAATLDGLGMLVEQAAESFNAWRGVRPESAPVISRIRDSL 271 *************************999******************************9999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (279 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: 00:00:00.03 # Mc/sec: 2.13 // [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