Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_028315506.1 G491_RS0117445 shikimate dehydrogenase
Query= SwissProt::Q5KWX7 (276 letters) >NCBI__GCF_000429905.1:WP_028315506.1 Length = 274 Score = 203 bits (517), Expect = 3e-57 Identities = 115/270 (42%), Positives = 160/270 (59%), Gaps = 10/270 (3%) Query: 1 MEKVYGLIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVN 60 + ++Y + G PV HSLSP MHN AF +G A Y F V V A+ +RA I G + Sbjct: 8 LTRLYAVFGDPVAHSLSPAMHNRAFTHIGENAAYMAFRVT--DVQGAVRAIRAFDIGGAS 65 Query: 61 VTIPHKLAVIPFLDEVDEHARRIGAVNTIINNDGRLVGYNTDGLGYVQALEEEMNITLDG 120 VTIPHK++V+ LDEVDE AR +GAVNTIIN+ GRL+G N+D LG V+A++E+ + Sbjct: 66 VTIPHKVSVMEHLDEVDETARAMGAVNTIINDQGRLIGKNSDCLGAVKAIQEKTPV--KD 123 Query: 121 KRILVIGAGGGARGIYFSLLSTAAERIDMANRTVEKAERLVREGDERRSAYFSLAEAETR 180 K ++VIGAGG AR + + L A R+ + NRT+EK RL E L + R Sbjct: 124 KDVVVIGAGGAARAVIYGLKQEGA-RVTIVNRTMEKGARLAEELGVDFQPMEDLGKLNCR 182 Query: 181 LAEYDIIINTTSVGMHPRVEVQPLSLERLRPGVIVSDIIYNPLETKWLKEAKARGARVQN 240 +A +N TSVGM P V+ P ++ DI+Y PL T++L +A+ G + + Sbjct: 183 IA-----VNATSVGMVPNVQDSPAPASFFNKDMVAMDIVYRPLLTRFLSDARNAGCTIVD 237 Query: 241 GVGMLVYQGALAFEKWTGQWPDVNRMKQLV 270 G+ M VYQGA FE WTG+ V +M++ V Sbjct: 238 GIAMFVYQGASQFEWWTGKEAPVAQMRETV 267 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: 210 Number of extensions: 14 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: 276 Length of database: 274 Length adjustment: 25 Effective length of query: 251 Effective length of database: 249 Effective search space: 62499 Effective search space used: 62499 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_028315506.1 G491_RS0117445 (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.27867.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-83 264.9 0.1 3.7e-83 264.8 0.1 1.0 1 lcl|NCBI__GCF_000429905.1:WP_028315506.1 G491_RS0117445 shikimate dehydro Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429905.1:WP_028315506.1 G491_RS0117445 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 264.8 0.1 3.7e-83 3.7e-83 2 268 .. 11 270 .. 10 272 .. 0.97 Alignments for each domain: == domain 1 score: 264.8 bits; conditional E-value: 3.7e-83 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 l++v+G+p++hS+sp++hn+a+ + g + Y+af v+ +++ a+ +i+a + G++vT+P+K++v+e lcl|NCBI__GCF_000429905.1:WP_028315506.1 11 LYAVFGDPVAHSLSPAMHNRAFTHIGENAAYMAFRVT--DVQGAVRAIRAFDIGGASVTIPHKVSVMEH 77 79********************************986..7999************************** PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlka 139 lDe++e+a+++gavNT+ ++g+l+g+n D +G+v+++++ +++k +k v++iGAGGaa+av+ L+++ lcl|NCBI__GCF_000429905.1:WP_028315506.1 78 LDEVDETARAMGAVNTIINDQGRLIGKNSDCLGAVKAIQEKTPVK-DKDVVVIGAGGAARAVIYGLKQE 145 ****************************************99999.*********************** PP TIGR00507 140 dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegk 208 + +v+i+NRt+ek+ +lae+l + ++e++ + + + +nats+g+ +++++ + +a+ +++++ lcl|NCBI__GCF_000429905.1:WP_028315506.1 146 GARVTIVNRTMEKGARLAEELGV----DFQPMEDLGKLNCRIAVNATSVGMVPNVQDSPAPASFFNKDM 210 **************999999977....788999************************************ PP TIGR00507 209 lvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkek 268 +++D+vy pl t +l+ a++ g+ ++dG+ M+v+Q+a +Fe wtg e +v +++e++++ lcl|NCBI__GCF_000429905.1:WP_028315506.1 211 VAMDIVYRPLLTRFLSDARNAGCTIVDGIAMFVYQGASQFEWWTGKEAPVAQMRETVETI 270 ******************************************************998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (274 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: 7.66 // [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