Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_012042045.1 BBTA_RS08420 shikimate dehydrogenase
Query= reanno::Caulo:CCNA_00003 (285 letters) >NCBI__GCF_000015165.1:WP_012042045.1 Length = 280 Score = 198 bits (503), Expect = 1e-55 Identities = 119/262 (45%), Positives = 154/262 (58%), Gaps = 3/262 (1%) Query: 16 GQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVRGLNVTIPFKER 75 G P HS SP+IH+ W+ G+ Y A + FV L G G NVTIP KER Sbjct: 14 GWPAAHSRSPLIHHHWLHKLGIAGGYTIEAVPPEELADFVTHLHGRGFVGANVTIPHKER 73 Query: 76 ALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTAAPVVIL 135 L + S AR GAAN L + E G + A NTD G +G + APG+D T +V L Sbjct: 74 VLELTKPDSR-ARAVGAANTLWY-EHGILRATNTDVEGFVGNLDAAAPGWDRTDVALV-L 130 Query: 136 GAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALLPEAGLI 195 G+GG+AR V LL G R+ V+NRT ARAQ LAD FG +VVA G + + ALLP+AGL+ Sbjct: 131 GSGGSARAVVFGLLERGIGRVHVINRTAARAQALADQFGPRVVAGGWEQVSALLPQAGLL 190 Query: 196 INATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTVDGLEMLLRQ 255 +N TSLG+ G + ++ P+ AVV+D+VY PL T+ L A A G RT DGL MLL Q Sbjct: 191 VNTTSLGMHGQPPLAIEIGRLPEQAVVVDIVYVPLETQLLVAARARGLRTADGLGMLLHQ 250 Query: 256 AIPTFETIYGQAPSPKIDVRVL 277 A+ FE +G+ P ++R L Sbjct: 251 AVRGFELWFGERPQVTPELRAL 272 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: 204 Number of extensions: 11 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 WP_012042045.1 BBTA_RS08420 (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.8938.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.3e-66 208.0 0.0 8.9e-66 207.8 0.0 1.0 1 lcl|NCBI__GCF_000015165.1:WP_012042045.1 BBTA_RS08420 shikimate dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015165.1:WP_012042045.1 BBTA_RS08420 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 207.8 0.0 8.9e-66 8.9e-66 4 262 .. 11 269 .. 8 276 .. 0.94 Alignments for each domain: == domain 1 score: 207.8 bits; conditional E-value: 8.9e-66 TIGR00507 4 gviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellD 72 +iG p +hS splih + l++lg+++ Y+ v++eel ++++ + g+ G+nvT+P+Ke+vlel lcl|NCBI__GCF_000015165.1:WP_012042045.1 11 CLIGWPAAHSRSPLIHHHWLHKLGIAGGYTIEAVPPEELADFVTHLHGRGFVGANVTIPHKERVLELT- 78 69****************************************************************99. PP TIGR00507 73 eieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka. 139 + + +a+++ga NTl e g l + nTD++G+v +L +l++G GG+a+av++ Ll+ lcl|NCBI__GCF_000015165.1:WP_012042045.1 79 KPDSRARAVGAANTLWYEHGILRATNTDVEGFVGNLDAaAPGWDRTDVALVLGSGGSARAVVFGLLERg 147 *************************************9644455578899****************994 PP TIGR00507 140 dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkegk 208 +v ++NRt ++a++la+++ +++ + l + l++n+ts+g++g+ +++ ++l e++ lcl|NCBI__GCF_000015165.1:WP_012042045.1 148 IGRVHVINRTAARAQALADQFGPRVVAGGWEQVSALLPQAGLLVNTTSLGMHGQP-PLAIEIGRLPEQA 215 569********************8888888888899999**************98.8999********* PP TIGR00507 209 lvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvf 262 +vvD+vy plet ll a+ +g +++dGlgMl +Qa+ Felw+g p+v lcl|NCBI__GCF_000015165.1:WP_012042045.1 216 VVVDIVYVPLETQLLVAARARGLRTADGLGMLLHQAVRGFELWFGERPQVTPEL 269 ***********************************************9998755 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.08 // [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