Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate BWI76_RS25645 BWI76_RS25645 shikimate dehydrogenase
Query= BRENDA::P15770 (272 letters) >FitnessBrowser__Koxy:BWI76_RS25645 Length = 272 Score = 437 bits (1125), Expect = e-128 Identities = 214/272 (78%), Positives = 242/272 (88%) Query: 1 METYAVFGNPIAHSKSPFIHQQFAQQLNIEHPYGRVLAPINDFINTLNAFFSAGGKGANV 60 METYAVFGNPIAHSKSP IH+ FAQQL I HPYGR+LAP++DF+ TL+AFF+ GGKGANV Sbjct: 1 METYAVFGNPIAHSKSPSIHRLFAQQLQITHPYGRILAPLDDFVTTLDAFFNEGGKGANV 60 Query: 61 TVPFKEEAFARADELTERAALAGAVNTLMRLEDGRLLGDNTDGVGLLSDLERLSFIRPGL 120 TVPFKEEAFARADELTERAALAGAVNTL RLEDGRLLGDNTDG+GLLSDLERL FI+PG Sbjct: 61 TVPFKEEAFARADELTERAALAGAVNTLKRLEDGRLLGDNTDGIGLLSDLERLGFIKPGF 120 Query: 121 RILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDELEGHE 180 R+LLIGAGGASRGVLLPLLSLDCAVTI NRT SRA ELA LF+HTGS++AL ++ L G E Sbjct: 121 RVLLIGAGGASRGVLLPLLSLDCAVTIVNRTYSRAHELATLFSHTGSVRALDIEALGGQE 180 Query: 181 FDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGM 240 FDLI+NATSSGI GD+P+IP +LI+P + CYDMFYQKG TPFLA C+Q G+ + ADGLGM Sbjct: 181 FDLIVNATSSGIDGDVPSIPVTLINPHVCCYDMFYQKGCTPFLALCQQHGATKCADGLGM 240 Query: 241 LVAQAAHAFLLWHGVLPDVEPVIKQLQEELSA 272 LVAQAAHA LLWHGVLP++ PVI LQ+EL+A Sbjct: 241 LVAQAAHAVLLWHGVLPEIRPVIAALQKELNA 272 Lambda K H 0.321 0.138 0.405 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: 314 Number of extensions: 9 Number of successful extensions: 1 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: 272 Length of database: 272 Length adjustment: 25 Effective length of query: 247 Effective length of database: 247 Effective search space: 61009 Effective search space used: 61009 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 BWI76_RS25645 BWI76_RS25645 (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.31226.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-102 328.2 0.0 1.9e-102 328.0 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS25645 BWI76_RS25645 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS25645 BWI76_RS25645 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 328.0 0.0 1.9e-102 1.9e-102 2 269 .. 3 270 .. 2 271 .. 0.99 Alignments for each domain: == domain 1 score: 328.0 bits; conditional E-value: 1.9e-102 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellD 72 +++v+Gnpi+hSksp ih +++ql+++++Y ++ ++++++ +l++++++g kG+nvTvPfKee+++++D lcl|FitnessBrowser__Koxy:BWI76_RS25645 3 TYAVFGNPIAHSKSPSIHRLFAQQLQITHPYGRILAPLDDFVTTLDAFFNEGGKGANVTVPFKEEAFARAD 73 89********************************************************************* PP TIGR00507 73 eieesakligavNTlk.ledgklvgynTDgiGlvssLeklsklksekrvliiGAGGaakavaleLlkadke 142 e++e+a+l+gavNTlk ledg+l+g+nTDgiGl+s+Le+l ++k++ rvl+iGAGGa+++v+l+Ll+ d++ lcl|FitnessBrowser__Koxy:BWI76_RS25645 74 ELTERAALAGAVNTLKrLEDGRLLGDNTDGIGLLSDLERLGFIKPGFRVLLIGAGGASRGVLLPLLSLDCA 144 *********************************************************************** PP TIGR00507 143 viiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegklvvDl 213 v+i+NRt ++a+ela + ++g++ al+ e + +++dli+nats+g+ g++ ++++ l++ +++D+ lcl|FitnessBrowser__Koxy:BWI76_RS25645 145 VTIVNRTYSRAHELATLFSHTGSVRALDIEALGGQEFDLIVNATSSGIDGDV--PSIPVTLINPHVCCYDM 213 ****************************************************..999999*********** PP TIGR00507 214 vynpletpllkeakkkg.tkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 +y+++ tp+l++++++g tk +dGlgMlvaQaa++ lw+gv+p++ v+ al+++l lcl|FitnessBrowser__Koxy:BWI76_RS25645 214 FYQKGCTPFLALCQQHGaTKCADGLGMLVAQAAHAVLLWHGVLPEIRPVIAALQKEL 270 *****************9***********************************9988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (272 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: 10.59 // [ok]
This GapMind analysis is from Apr 09 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