Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_092997956.1 BLP65_RS12860 shikimate dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_900102855.1:WP_092997956.1 Length = 282 Score = 286 bits (733), Expect = 3e-82 Identities = 158/273 (57%), Positives = 183/273 (67%), Gaps = 4/273 (1%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGG-NVT 60 D Y V GNPI HSKSP IH LFAEQTGQ L Y +L F F G G NVT Sbjct: 11 DAYAVMGNPIAHSKSPRIHALFAEQTGQRLTYTAILVEPGGFDQAVGNFQANGGKGLNVT 70 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFK+EA+RL D +PRA RAGAVNT++ DG+ GDNTDG GLV DL+ GV L G Sbjct: 71 VPFKQEAWRLVDRRSPRAERAGAVNTVTLHEDGSRSGDNTDGIGLVNDLS-RLGVTLTGC 129 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQ-E 179 R+LILGAGGAVRGVLEP+L P L IANRTV +AE+LA F +G V GF L+ Sbjct: 130 RVLILGAGGAVRGVLEPLLDQGPAELWIANRTVARAEELASAFASMGTVNGCGFDDLKGR 189 Query: 180 PVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGL 239 DVIIN T+ASL GE+PP+ D+++ CYDMMY PT F QWA + GA DGL Sbjct: 190 QFDVIINGTAASLQGEVPPLPDTVLGKDGA-CYDMMYAARPTAFIQWARRHGATAAHDGL 248 Query: 240 GMLAEQAAEAFFIWRGVRPDTAPVLAELRRQLA 272 GML QAAE+FFIWRGVRP+T PV+ LRR+LA Sbjct: 249 GMLVAQAAESFFIWRGVRPETGPVIEALRRELA 281 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: 8 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: 274 Length of database: 282 Length adjustment: 25 Effective length of query: 249 Effective length of database: 257 Effective search space: 63993 Effective search space used: 63993 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_092997956.1 BLP65_RS12860 (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.20735.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-86 275.4 0.0 2.4e-86 275.2 0.0 1.0 1 lcl|NCBI__GCF_900102855.1:WP_092997956.1 BLP65_RS12860 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900102855.1:WP_092997956.1 BLP65_RS12860 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 275.2 0.0 2.4e-86 2.4e-86 2 269 .. 12 280 .. 11 281 .. 0.98 Alignments for each domain: == domain 1 score: 275.2 bits; conditional E-value: 2.4e-86 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++v+Gnpi+hSksp ih +++q+g+ l+Y+a+ ve+ + +a+ +++a+g kG+nvTvPfK+e+ +l lcl|NCBI__GCF_900102855.1:WP_092997956.1 12 AYAVMGNPIAHSKSPRIHALFAEQTGQRLTYTAILVEPGGFDQAVGNFQANGGKGLNVTVPFKQEAWRL 80 69******************************************************************* PP TIGR00507 71 lDeieesakligavNTlk.ledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlk 138 +D+ +++a+ +gavNT++ edg g+nTDgiGlv +L++l ++ rvli+GAGGa ++v+ +Ll+ lcl|NCBI__GCF_900102855.1:WP_092997956.1 81 VDRRSPRAERAGAVNTVTlHEDGSRSGDNTDGIGLVNDLSRLGVTLTGCRVLILGAGGAVRGVLEPLLD 149 ******************778999*****************998888********************** PP TIGR00507 139 a.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellke 206 + + e+ iaNRtv++aeela++++++g++ ++++ +++d+iin t+a+l+ge+ ++++ +l + lcl|NCBI__GCF_900102855.1:WP_092997956.1 150 QgPAELWIANRTVARAEELASAFASMGTVNGCGFDDLKGRQFDVIINGTAASLQGEV--PPLPDTVLGK 216 9889*****************************************************..********** PP TIGR00507 207 gklvvDlvynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 + +++D++y+ t+++++a+++g t dGlgMlvaQaa sF +w+gv p+ v+eal+++l lcl|NCBI__GCF_900102855.1:WP_092997956.1 217 DGACYDMMYAARPTAFIQWARRHGaTAAHDGLGMLVAQAAESFFIWRGVRPETGPVIEALRREL 280 ************************9999********************************9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (282 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: 00:00:00.00 # Mc/sec: 8.65 // [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