Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate YP_004140082.1 Mesci_0866 shikimate 5-dehydrogenase
Query= reanno::Caulo:CCNA_00003 (285 letters) >NCBI__GCF_000185905.1:YP_004140082.1 Length = 280 Score = 208 bits (530), Expect = 9e-59 Identities = 120/264 (45%), Positives = 152/264 (57%), Gaps = 2/264 (0%) Query: 14 VCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVRGLNVTIPFK 73 V G P+KHS SP IH W+A G+D +Y A F FV+ L+ RG N+TIP K Sbjct: 10 VSGHPVKHSRSPKIHGHWLAKHGIDGSYQAIDVAPQDFAVFVETLQANNYRGGNITIPHK 69 Query: 74 ERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTAAPVV 133 E A A+A+ A+ GA N L F EDG + NTDG G + APG+ + P V Sbjct: 70 EAAFALAERRDQAAQEIGAVNTLWF-EDGVLWGGNTDGHGFAANLDDHAPGW-ASKGPAV 127 Query: 134 ILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALLPEAG 193 +LGAGGA+R + AL G I +VNRT+ARAQ+L D FG V A G A LL +AG Sbjct: 128 VLGAGGASRAVIHALKERGVADIRIVNRTLARAQELRDRFGTGVSAHGMAATNELLGDAG 187 Query: 194 LIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTVDGLEMLL 253 L++N T+LG+ G G SAD P A+V D+VY PL T L A A +TVDGL MLL Sbjct: 188 LLVNTTALGMHGNEGLSADPARLPDHAIVTDIVYVPLETPLLAAARARNLKTVDGLGMLL 247 Query: 254 RQAIPTFETIYGQAPSPKIDVRVL 277 QA+P FE +G P ++R L Sbjct: 248 HQAVPGFERWFGIRPRVTAELRAL 271 Lambda K H 0.319 0.136 0.390 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: 206 Number of extensions: 9 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: 285 Length of database: 280 Length adjustment: 26 Effective length of query: 259 Effective length of database: 254 Effective search space: 65786 Effective search space used: 65786 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 YP_004140082.1 Mesci_0866 (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.22025.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-69 218.7 0.0 5e-69 218.4 0.0 1.0 1 lcl|NCBI__GCF_000185905.1:YP_004140082.1 Mesci_0866 shikimate 5-dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185905.1:YP_004140082.1 Mesci_0866 shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 218.4 0.0 5e-69 5e-69 5 260 .. 10 266 .. 6 274 .. 0.94 Alignments for each domain: == domain 1 score: 218.4 bits; conditional E-value: 5e-69 TIGR00507 5 viGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDe 73 v G+p+khS sp ih + l++ g+++ Y a++v ++++ ++++++a+ +G n+T+P+Ke++++l+++ lcl|NCBI__GCF_000185905.1:YP_004140082.1 10 VSGHPVKHSRSPKIHGHWLAKHGIDGSYQAIDVAPQDFAVFVETLQANNYRGGNITIPHKEAAFALAER 78 78******************************************************************* PP TIGR00507 74 ieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka.d 140 ++ a++igavNTl edg l g nTDg G+ ++L s+ ++++GAGGa++av+ +L++ lcl|NCBI__GCF_000185905.1:YP_004140082.1 79 RDQAAQEIGAVNTLWFEDGVLWGGNTDGHGFAANLDDhAPGWASKGPAVVLGAGGASRAVIHALKERgV 147 ************************************97666677999******************9955 PP TIGR00507 141 keviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegkl 209 ++ i+NRt+++a+el +r+ + + + + l l++n+t++g++g+ + ++ +l ++ lcl|NCBI__GCF_000185905.1:YP_004140082.1 148 ADIRIVNRTLARAQELRDRFGTGVSAHGMAATNELLGDAGLLVNTTALGMHGNE-GLSADPARLPDHAI 215 78********************7788888888888888***************9.9999999******* PP TIGR00507 210 vvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvek 260 v D+vy pletpll+ a+ ++ k++dGlgMl +Qa+ Fe w+g+ p v lcl|NCBI__GCF_000185905.1:YP_004140082.1 216 VTDIVYVPLETPLLAAARARNLKTVDGLGMLLHQAVPGFERWFGIRPRVTA 266 **********************************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (280 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: 00:00:00.00 # Mc/sec: 9.99 // [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