Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_092350824.1 BLU87_RS16360 shikimate dehydrogenase
Query= SwissProt::Q5KWX7 (276 letters) >NCBI__GCF_900107645.1:WP_092350824.1 Length = 283 Score = 209 bits (532), Expect = 5e-59 Identities = 118/276 (42%), Positives = 168/276 (60%), Gaps = 9/276 (3%) Query: 3 KVYGLIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVNVT 62 +VYGL+G PV HSLSPLM N AF I A Y F V P + AA+AG+RAL IAGVNVT Sbjct: 8 RVYGLLGDPVAHSLSPLMQNHAFQFHAIDAVYTPFHVAPDDLPAAVAGLRALDIAGVNVT 67 Query: 63 IPHKLAVIPFLDEVDEHARRIGAVNTIINNDGRLVGYNTDGLGYVQALEEEMNITLDGKR 122 IPHK A++P LD +D A+ IGAVNT++N +G L GYNTD G+++A+++E+ G+ Sbjct: 68 IPHKEAILPLLDRIDPAAQLIGAVNTVVNKNGILSGYNTDASGFIKAVQQELTFCPTGRN 127 Query: 123 ILVIGAGGGARGIYFSLLSTAAERIDMANRTVEKAERLVRE-------GDERRSAYFSLA 175 ++V+GAGG R +L+S + I +ANR +A LV + D + Y Sbjct: 128 VVVLGAGGACRACVVALVSAGVKSITVANRHKSRAVELVNDLQLHFPTVDFYAADYLDPF 187 Query: 176 EAETRLAEYDIIINTTSVGMHPRVEVQPLSLERLRPGVIVSDIIYNPLETKWLKEAKARG 235 ++ L+ D+I+NTTSVG+H V L LE ++ ++ D++Y+P ET LK A+ G Sbjct: 188 YRQS-LSLADLIVNTTSVGLHGE-SVNFLPLENIKCSALIFDMVYSPSETPLLKNARLAG 245 Query: 236 ARVQNGVGMLVYQGALAFEKWTGQWPDVNRMKQLVI 271 +G+GML QG AF WTG P M++ ++ Sbjct: 246 HLCADGLGMLAAQGEDAFFLWTGIRPPSGFMRKTLV 281 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: 194 Number of extensions: 7 Number of successful extensions: 3 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: 283 Length adjustment: 26 Effective length of query: 250 Effective length of database: 257 Effective search space: 64250 Effective search space used: 64250 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_092350824.1 BLU87_RS16360 (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.26628.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-77 244.2 0.0 8.8e-77 243.9 0.0 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092350824.1 BLU87_RS16360 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092350824.1 BLU87_RS16360 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 243.9 0.0 8.8e-77 8.8e-77 2 265 .. 9 280 .. 8 282 .. 0.92 Alignments for each domain: == domain 1 score: 243.9 bits; conditional E-value: 8.8e-77 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++g++G+p++hS+spl++n+a++ ++ +Y+ f+v +++l+ a+ g++al + GvnvT+P+Ke++l+l lcl|NCBI__GCF_900107645.1:WP_092350824.1 9 VYGLLGDPVAHSLSPLMQNHAFQFHAIDAVYTPFHVAPDDLPAAVAGLRALDIAGVNVTIPHKEAILPL 77 79******************************************************************* PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlk 138 lD+i++ a+ligavNT++ ++g l gynTD+ G++++ ++ l++ ++++v+++GAGGa +a +++L++ lcl|NCBI__GCF_900107645.1:WP_092350824.1 78 LDRIDPAAQLIGAVNTVVNKNGILSGYNTDASGFIKAVQQeLTFCPTGRNVVVLGAGGACRACVVALVS 146 ********************************************************************* PP TIGR00507 139 a.dkeviiaNRtvekaeelaerlqe.......lgeilalsleevelkkvdliinatsaglsgeideaev 199 a k++++aNR +++a el++ lq + + + + l+ dli+n+ts+gl+ge + lcl|NCBI__GCF_900107645.1:WP_092350824.1 147 AgVKSITVANRHKSRAVELVNDLQLhfptvdfYAADYLDPFYRQSLSLADLIVNTTSVGLHGES-VNFL 214 *5688*****************998644444333333333334445559**************9.6789 PP TIGR00507 200 kaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfeal 265 + e +k ++l++D+vy p etpllk a+ g +dGlgMl aQ+ +F lwtg+ p+ ++++l lcl|NCBI__GCF_900107645.1:WP_092350824.1 215 PLENIKCSALIFDMVYSPSETPLLKNARLAGHLCADGLGMLAAQGEDAFFLWTGIRPPSGFMRKTL 280 *********************************************************999998865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (283 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.13 // [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