Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_028988545.1 G579_RS0100030 shikimate dehydrogenase
Query= SwissProt::Q5KWX7 (276 letters) >NCBI__GCF_000423825.1:WP_028988545.1 Length = 290 Score = 183 bits (464), Expect = 4e-51 Identities = 110/267 (41%), Positives = 152/267 (56%), Gaps = 4/267 (1%) Query: 4 VYGLIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVNVTI 63 VYG++G PV HSLSPLMH +G Y F V AA+AG+ ALG+ GVNVT+ Sbjct: 12 VYGIVGDPVAHSLSPLMHAAFAEAVGADLVYVPFHVREAHFAAALAGLPALGVCGVNVTV 71 Query: 64 PHKLAVIPFLDEVDEHARRIGAVNTIINNDGRLVGYNTDGLGYVQALEEEMNITLDGKRI 123 PHK E+ A IGAVNT+ DGR++G+NTD G+ AL ++ + G+ Sbjct: 72 PHKERAHALAQELTPEAAGIGAVNTLHFVDGRVLGHNTDAAGFSLAL-DDTGLDWRGRTA 130 Query: 124 LVIGAGGGARGIYFSLLSTAAERIDMANRTVEKAERLVREGDERRSAYFSLAEAETR--L 181 LVIGAGG AR I ++L ++ A I +ANRT+ +AE L + L L Sbjct: 131 LVIGAGGAARAILWALGASGATAIHLANRTLARAEALAAAFPQFPIHPLPLDRDHLTPLL 190 Query: 182 AEYDIIINTTSVGMHPRVEVQPLSLERLRPGVIVSDIIYNPLETKWLKEAKARGARVQNG 241 E +++NT+S G+H + L L RL I+ DI+YNP+ T L A + G R +G Sbjct: 191 HEVGLVVNTSSRGLHGEGHPE-LELARLPKTGIICDIVYNPISTPLLAAANSMGLRTVDG 249 Query: 242 VGMLVYQGALAFEKWTGQWPDVNRMKQ 268 +GML++QGA +F WTGQ P V +K+ Sbjct: 250 LGMLLHQGAASFRLWTGQQPPVAAVKE 276 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: 240 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: 276 Length of database: 290 Length adjustment: 26 Effective length of query: 250 Effective length of database: 264 Effective search space: 66000 Effective search space used: 66000 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_028988545.1 G579_RS0100030 (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.19304.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-79 250.8 0.0 7.4e-79 250.6 0.0 1.0 1 lcl|NCBI__GCF_000423825.1:WP_028988545.1 G579_RS0100030 shikimate dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000423825.1:WP_028988545.1 G579_RS0100030 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.6 0.0 7.4e-79 7.4e-79 2 269 .. 12 282 .. 11 283 .. 0.93 Alignments for each domain: == domain 1 score: 250.6 bits; conditional E-value: 7.4e-79 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++g++G+p++hS+spl+h a+++ g +l+Y+ f+v++ ++ al g+ alg+ GvnvTvP+Ke++ +l lcl|NCBI__GCF_000423825.1:WP_028988545.1 12 VYGIVGDPVAHSLSPLMHAAFAEAVGADLVYVPFHVREAHFAAALAGLPALGVCGVNVTVPHKERAHAL 80 79******************************************************************* PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 + e++++a+ igavNTl+ dg+++g+nTD+ G+ +L ++++l+iGAGGaa+a++ +L lcl|NCBI__GCF_000423825.1:WP_028988545.1 81 AQELTPEAAGIGAVNTLHFVDGRVLGHNTDAAGFSLALDDTGLDWRGRTALVIGAGGAARAILWALGAS 149 ***************************************94433348*******************988 PP TIGR00507 140 .dkeviiaNRtvekaeelaerlqelg.eilalsleeve..lkkvdliinatsaglsgeideaevkaell 204 +++ +aNRt+++ae+la +++++ + l l+ +++ l++v l++n+ s gl+ge ++e++ +l lcl|NCBI__GCF_000423825.1:WP_028988545.1 150 gATAIHLANRTLARAEALAAAFPQFPiHPLPLDRDHLTplLHEVGLVVNTSSRGLHGEG-HPELELARL 217 57899*******************5413455566665433578***************9.99******* PP TIGR00507 205 kegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 + +++D+vynp+ tpll+ a++ g +++dGlgMl +Q+a sF+lwtg++p+v v+e+l++ l lcl|NCBI__GCF_000423825.1:WP_028988545.1 218 PKTGIICDIVYNPISTPLLAAANSMGLRTVDGLGMLLHQGAASFRLWTGQQPPVAAVKEKLEQWL 282 **********************************************************9988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (290 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: 00:00:00.01 # Mc/sec: 7.67 // [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