Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_012502877.1 CPAR_RS08355 shikimate dehydrogenase
Query= SwissProt::Q58484 (282 letters) >NCBI__GCF_000020505.1:WP_012502877.1 Length = 296 Score = 191 bits (484), Expect = 2e-53 Identities = 117/290 (40%), Positives = 174/290 (60%), Gaps = 23/290 (7%) Query: 7 KVIGLIGHPVEHSFSPIMHNAAFKDKGLNYVYVAFDVL-PENLKYVIDGAKALGIVGFNV 65 KV GLIG V++S+SP++HN AF+ GL +Y F++ PE + + GA+ALGI GFNV Sbjct: 8 KVFGLIGRNVDYSWSPLIHNTAFQALGLPSIYTIFNIAAPELVGNALTGARALGIAGFNV 67 Query: 66 TIPHKIEIMKYLDEIDKDAQLIGAVNTIKIEDGKAIGYNTDGIGARMALEEEIGRVKDKN 125 TIP+K ++ +LDE+ +AQ IGAVNTI ++G+ G+NTD G L ++ K Sbjct: 68 TIPYKKTVVPFLDELSPEAQAIGAVNTIVNDNGRLTGHNTDIAGFAAPLLPMAEQIHGKP 127 Query: 126 IVIYGAGGAARAV--AFEL-AKDNNIIIANRTVEKAEALAKEIAEKLNKKFGEEVKFSGL 182 + I+G GGAA A AF L +++ + R +EKAEA+ + A + E+ L Sbjct: 128 VCIFGNGGAALAAVEAFRLHFHPSSVRLMVRNLEKAEAMLEGYAHR-------ELVEPCL 180 Query: 183 DVDLDGVD---------IIINATPIGMYPNID-VEPIVKAEK--LREDMVVMDLIYNPLE 230 +LD D +I+NATPIG D ++ +V A + L E +V D++YNPLE Sbjct: 181 TAELDTPDGERLLGECCVIVNATPIGTAGRSDAIQSVVPARRKLLHEGQIVYDMVYNPLE 240 Query: 231 TVLLKEAKKVNAKTINGLGMLIYQGAVAFKIWTGVEPNIEVMKNAIIDKI 280 T LL EA+ A+TI+G+ MLI Q A +F IWTG E ++ ++ ++D+I Sbjct: 241 TPLLAEARAAGAETISGIEMLIGQAARSFSIWTGQEMPVDTVRKTVLDEI 290 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: 201 Number of extensions: 12 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: 296 Length adjustment: 26 Effective length of query: 256 Effective length of database: 270 Effective search space: 69120 Effective search space used: 69120 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: 48 (23.1 bits)
Align candidate WP_012502877.1 CPAR_RS08355 (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.18245.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-71 226.9 0.0 1.4e-71 226.7 0.0 1.0 1 lcl|NCBI__GCF_000020505.1:WP_012502877.1 CPAR_RS08355 shikimate dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020505.1:WP_012502877.1 CPAR_RS08355 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 226.7 0.0 1.4e-71 1.4e-71 1 269 [. 8 290 .. 8 291 .. 0.90 Alignments for each domain: == domain 1 score: 226.7 bits; conditional E-value: 1.4e-71 TIGR00507 1 kllgviGnpikhSksplihnaalkqlgleleYlafeve.ieelekalsgikalglkGvnvTvPfKeevl 68 k++g+iG + S splihn a++ lgl Y+ f++ +e + +al+g++alg+ G+nvT+P+K+ v+ lcl|NCBI__GCF_000020505.1:WP_012502877.1 8 KVFGLIGRNVDYSWSPLIHNTAFQALGLPSIYTIFNIAaPELVGNALTGARALGIAGFNVTIPYKKTVV 76 689********************************986155589************************* PP TIGR00507 69 ellDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakav..ale 135 ++lDe++++a++igavNT++ ++g+l g+nTD G+ + L + + +k v i G GGaa a+ a++ lcl|NCBI__GCF_000020505.1:WP_012502877.1 77 PFLDELSPEAQAIGAVNTIVNDNGRLTGHNTDIAGFAAPLLPMAEQIHGKPVCIFGNGGAALAAveAFR 145 ****************************************99666666*************99845688 PP TIGR00507 136 LlkadkeviiaNRtvekaeelaerlqe...lgeilalsleevelkk....vdliinatsaglsgeid.. 195 L ++++v ++ R +ekae+++e ++ + +l+ +l+ + ++ +i+nat++g g d lcl|NCBI__GCF_000020505.1:WP_012502877.1 146 LHFHPSSVRLMVRNLEKAEAMLEGYAHrelVEPCLTAELDTPDGERllgeCCVIVNATPIGTAGRSDai 214 8889*******************99997875556666666555555544589***********999865 PP TIGR00507 196 eaevka..ellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvf 262 + v+a +ll+eg++v+D+vynpletpll+ea+ g+++i G++Ml+ Qaa sF +wtg+e +v+ v+ lcl|NCBI__GCF_000020505.1:WP_012502877.1 215 QSVVPArrKLLHEGQIVYDMVYNPLETPLLAEARAAGAETISGIEMLIGQAARSFSIWTGQEMPVDTVR 283 5555542278*********************************************************** PP TIGR00507 263 ealkekl 269 +++ +++ lcl|NCBI__GCF_000020505.1:WP_012502877.1 284 KTVLDEI 290 9998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (296 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: 11.21 // [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