Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_011190253.1 DP_RS15245 shikimate dehydrogenase
Query= SwissProt::Q5KWX7 (276 letters) >NCBI__GCF_000025945.1:WP_011190253.1 Length = 296 Score = 200 bits (508), Expect = 3e-56 Identities = 123/260 (47%), Positives = 166/260 (63%), Gaps = 14/260 (5%) Query: 4 VYGLIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVNVTI 63 VYG+IG PV HS+SPLMHN AF LGI A Y F VE V +A+ G+R L I GV+VTI Sbjct: 21 VYGIIGNPVSHSMSPLMHNAAFESLGIDAVYVPFRVE--DVESAVQGLRGLNICGVSVTI 78 Query: 64 PHKLAVIPFLDEVDEHARRIGAVNTIINN--DGR--LVGYNTDGLGYVQALEEEMNITLD 119 PHK AVIP LDEVD A +IGAVNTI+++ DGR L G+NTD +G +AL+ ++L Sbjct: 79 PHKEAVIPLLDEVDPVAGKIGAVNTIVSSMRDGRPFLKGFNTDWIGANRALQAV--VSLK 136 Query: 120 GKRILVIGAGGGARGIYFSLLSTAAERIDMANRTVEKAERLVREGDERRSAYFSLAEAET 179 GK++L++GAGG AR I F LL AE I + +RT + +L DE + SL + + Sbjct: 137 GKQVLLLGAGGSARAIGFGLLEAGAEVI-LCSRTPSRGRQLA---DEFGCLWLSLEDIGS 192 Query: 180 RLAEYDIIINTTSVGMHPRVEVQPLSLERLRPGVIVSDIIYNPLETKWLKEAKARGARVQ 239 A DI++N TSVGM P+ +V +++E+L V DI+Y+P T+ L A G + Sbjct: 193 VRA--DIVVNATSVGMAPQEDVSLMTVEQLSGVEAVMDIVYSPHRTRLLANADKAGCAIV 250 Query: 240 NGVGMLVYQGALAFEKWTGQ 259 +G+ ML+YQG FE W G+ Sbjct: 251 SGLEMLLYQGVQQFELWQGR 270 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: 217 Number of extensions: 10 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: 276 Length of database: 296 Length adjustment: 26 Effective length of query: 250 Effective length of database: 270 Effective search space: 67500 Effective search space used: 67500 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_011190253.1 DP_RS15245 (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.23981.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-77 246.3 0.0 1.8e-77 246.1 0.0 1.0 1 lcl|NCBI__GCF_000025945.1:WP_011190253.1 DP_RS15245 shikimate dehydrogena Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025945.1:WP_011190253.1 DP_RS15245 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.1 0.0 1.8e-77 1.8e-77 2 267 .. 21 283 .. 20 286 .. 0.97 Alignments for each domain: == domain 1 score: 246.1 bits; conditional E-value: 1.8e-77 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++g+iGnp+ hS+spl+hnaa++ lg++ +Y+ f v e++e+a++g++ l + Gv+vT+P+Ke+v++l lcl|NCBI__GCF_000025945.1:WP_011190253.1 21 VYGIIGNPVSHSMSPLMHNAAFESLGIDAVYVPFRV--EDVESAVQGLRGLNICGVSVTIPHKEAVIPL 87 79*****************************99876..6899*************************** PP TIGR00507 71 lDeieesakligavNTlk..ledgk..lvgynTDgiGlvssLeklsklksekrvliiGAGGaakavale 135 lDe+++ a +igavNT++ ++dg+ l g nTD iG+ +L+ + lk +k+vl++GAGG+a+a+ + lcl|NCBI__GCF_000025945.1:WP_011190253.1 88 LDEVDPVAGKIGAVNTIVssMRDGRpfLKGFNTDWIGANRALQAVVSLK-GKQVLLLGAGGSARAIGFG 155 *****************9999***98899********************.******************* PP TIGR00507 136 LlkadkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaell 204 Ll+a+ evi++ Rt +++++la+++ l lsle++ + d+++nats+g+ ++ d ++ e l lcl|NCBI__GCF_000025945.1:WP_011190253.1 156 LLEAGAEVILCSRTPSRGRQLADEFGC----LWLSLEDIGSVRADIVVNATSVGMAPQEDVSLMTVEQL 220 ***********************9976....99**************************9889999*** PP TIGR00507 205 kegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealke 267 + ++v+D+vy p t ll+ a k g+ ++ Gl+Ml +Q++++Felw+g e ++ +++++l + lcl|NCBI__GCF_000025945.1:WP_011190253.1 221 SGVEAVMDIVYSPHRTRLLANADKAGCAIVSGLEMLLYQGVQQFELWQGREAPLAVMRHTLYR 283 *********************************************************998765 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.13 // [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