Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate H281DRAFT_06291 H281DRAFT_06291 shikimate dehydrogenase (EC 1.1.1.25)
Query= BRENDA::Q88RQ5 (274 letters) >FitnessBrowser__Burk376:H281DRAFT_06291 Length = 287 Score = 267 bits (683), Expect = 2e-76 Identities = 153/277 (55%), Positives = 181/277 (65%), 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 DRYAVIGNPVGHSKSPFIHSRFAAQTGEPVEYSALLAPVDAFVPHVRAFIEAGGRGLNVT 67 Query: 61 VPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAGK 120 VPFK +A SL+PRA AGAVNTL ++ + GDNTDG GLVRD+ VN GV L G Sbjct: 68 VPFKLDAHAFASSLSPRAAAAGAVNTL-RIDPNGVYGDNTDGFGLVRDIEVNLGVSLKGA 126 Query: 121 RILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVA----SGFAW 176 RIL+LGAGGA RGV+ P+L P +L I NRT KAE L +F + VA G A Sbjct: 127 RILLLGAGGAARGVVLPMLERAPHTLTIVNRTAAKAEALVDQFAQAASGVACRLSGGNAR 186 Query: 177 LQEP--VDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAK 234 EP DVI+NAT+ SL LP D G T+ YDMMYG PT F + A KLG A+ Sbjct: 187 AIEPGAYDVIVNATAGSLEASLPECDDGAFGNG-TLAYDMMYGAHPTVFMEHAQKLG-AR 244 Query: 235 VLDGLGMLAEQAAEAFFIWRGVRPDTAPVLAELRRQL 271 DGLGML EQAAE+F++WRGVRPD+ PVLAELR L Sbjct: 245 GADGLGMLVEQAAESFYVWRGVRPDSVPVLAELRALL 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: 260 Number of extensions: 12 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 H281DRAFT_06291 H281DRAFT_06291 (shikimate dehydrogenase (EC 1.1.1.25))
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.3887.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-78 247.5 0.0 7.9e-78 247.3 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_06291 H281DRAFT_06291 shikimate dehydr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_06291 H281DRAFT_06291 shikimate dehydrogenase (EC 1.1.1.25) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 247.3 0.0 7.9e-78 7.9e-78 3 267 .. 10 279 .. 8 282 .. 0.93 Alignments for each domain: == domain 1 score: 247.3 bits; conditional E-value: 7.9e-78 TIGR00507 3 lgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevl 68 ++viGnp+ hSksp+ih ++++q+g +eY a+ ++++++ + ++ ++g +G+nvTvPfK + lcl|FitnessBrowser__Burk376:H281DRAFT_06291 10 YAVIGNPVGHSKSPFIHSRFAAQTGEPVEYSALLAPVDAFVPHVRAFIEAGGRGLNVTVPFKLDAH 75 9***************************************************************** PP TIGR00507 69 ellDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakava 133 +++ ++++a+++gavNTl+++ + ++g+nTDg Glv ++e l ++ r+l++GAGGaa++v+ lcl|FitnessBrowser__Burk376:H281DRAFT_06291 76 AFASSLSPRAAAAGAVNTLRIDPNGVYGDNTDGFGLVRDIEVnLGVSLKGARILLLGAGGAARGVV 141 *****************************************98887666***************** PP TIGR00507 134 leLlka.dkeviiaNRtvekaeelaerlqe..lgeilalsl...eevelkkvdliinatsaglsge 193 l++l+ +++++i+NRt +kae+l++++++ g + ls +e+ +d+i+nat+ +l+ lcl|FitnessBrowser__Burk376:H281DRAFT_06291 142 LPMLERaPHTLTIVNRTAAKAEALVDQFAQaaSGVACRLSGgnaRAIEPGAYDVIVNATAGSLEAS 207 *977654*********************99666777777751114566777*************** PP TIGR00507 194 ideaevkaellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdve 259 + +e + + + +g+l++D++y t++++ a+k+g++ +dGlgMlv+Qaa sF +w+gv pd lcl|FitnessBrowser__Burk376:H281DRAFT_06291 208 L--PECDDGAFGNGTLAYDMMYGAHPTVFMEHAQKLGARGADGLGMLVEQAAESFYVWRGVRPDSV 271 *..99***********************************************************99 PP TIGR00507 260 kvfealke 267 v l++ lcl|FitnessBrowser__Burk376:H281DRAFT_06291 272 PVLAELRA 279 99887766 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: 9.66 // [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