Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate BPHYT_RS16975 BPHYT_RS16975 shikimate 5-dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >FitnessBrowser__BFirm:BPHYT_RS16975 Length = 287 Score = 265 bits (678), Expect = 6e-76 Identities = 154/277 (55%), Positives = 179/277 (64%), Gaps = 10/277 (3%) Query: 2 DQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGSGG-NVT 60 D+Y V GNP+GHSKSP IH FA QTG+ +EY LLAP+D F R F G G NVT Sbjct: 8 DRYAVIGNPVGHSKSPFIHGRFAAQTGEAVEYGHLLAPVDAFVPHVRAFIDAGGRGLNVT 67 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFK +A D+L+PRA AGAVNTL A+G + GDNTDG GLVRD+ VN GV L G Sbjct: 68 VPFKLDAHAFADTLSPRAAAAGAVNTLRFDANG-IYGDNTDGFGLVRDIEVNLGVSLKGA 126 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVA------SGF 174 RIL+LGAGGA RGV+ P+L P +L I NRT EKAE L +F + A S Sbjct: 127 RILLLGAGGAARGVVLPMLDRAPHTLTIVNRTAEKAEALVAQFAQAARDAACQLSGGSAR 186 Query: 175 AWLQEPVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAK 234 A DVI+NAT+ SL LP D G T+ YDMMYG PT F + A KLG A+ Sbjct: 187 AIEAGTYDVIVNATAGSLDASLPECDDRAFGNG-TLAYDMMYGAHPTVFMEHARKLG-AR 244 Query: 235 VLDGLGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQL 271 DGLGML EQAAE+F++WRGVRPD APVLAELR L Sbjct: 245 GADGLGMLVEQAAESFYVWRGVRPDGAPVLAELRALL 281 Lambda K H 0.319 0.137 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: 264 Number of extensions: 13 Number of successful extensions: 6 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: 274 Length of database: 287 Length adjustment: 26 Effective length of query: 248 Effective length of database: 261 Effective search space: 64728 Effective search space used: 64728 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 BPHYT_RS16975 BPHYT_RS16975 (shikimate 5-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.16871.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-78 249.2 0.0 2.3e-78 249.1 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS16975 BPHYT_RS16975 shikimate 5-dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS16975 BPHYT_RS16975 shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.1 0.0 2.3e-78 2.3e-78 3 267 .. 10 279 .. 8 282 .. 0.92 Alignments for each domain: == domain 1 score: 249.1 bits; conditional E-value: 2.3e-78 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellD 72 ++viGnp+ hSksp+ih ++++q+g ++eY ++ ++++++ + ++ +g +G+nvTvPfK + +++D lcl|FitnessBrowser__BFirm:BPHYT_RS16975 10 YAVIGNPVGHSKSPFIHGRFAAQTGEAVEYGHLLAPVDAFVPHVRAFIDAGGRGLNVTVPFKLDAHAFAD 79 9********************************************************************* PP TIGR00507 73 eieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.d 140 ++++a+++gavNTl+ + + ++g+nTDg Glv ++e l ++ r+l++GAGGaa++v+l++l+ + lcl|FitnessBrowser__BFirm:BPHYT_RS16975 80 TLSPRAAAAGAVNTLRFDANGIYGDNTDGFGLVRDIEVnLGVSLKGARILLLGAGGAARGVVLPMLDRaP 149 *************************************98887666******************9886659 PP TIGR00507 141 keviiaNRtvekaeelaerlqe..lgeilal...sleevelkkvdliinatsaglsgeideaevkaellk 205 ++++i+NRt ekae+l+ ++++ ++l s +e ++d+i+nat+ +l + +e + + lcl|FitnessBrowser__BFirm:BPHYT_RS16975 150 HTLTIVNRTAEKAEALVAQFAQaaRDAACQLsggSARAIEAGTYDVIVNATAGSLDASL--PECDDRAFG 217 ********************99443333444111345678888****************..99******* PP TIGR00507 206 egklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealke 267 +g+l++D++y t++++ a+k+g++ +dGlgMlv+Qaa sF +w+gv pd v l++ lcl|FitnessBrowser__BFirm:BPHYT_RS16975 218 NGTLAYDMMYGAHPTVFMEHARKLGARGADGLGMLVEQAAESFYVWRGVRPDGAPVLAELRA 279 ***************************************************99888777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (287 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.22 // [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