Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate YP_002827835.1 NGR_c33520 shikimate 5-dehydrogenase
Query= reanno::Caulo:CCNA_00003 (285 letters) >NCBI__GCF_000018545.1:YP_002827835.1 Length = 286 Score = 193 bits (491), Expect = 3e-54 Identities = 119/269 (44%), Positives = 153/269 (56%), Gaps = 4/269 (1%) Query: 14 VCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVR--GLNVTIP 71 V G PIKHS SP+IH W+ G+ +Y + F F+ LR G G NVTIP Sbjct: 14 VTGYPIKHSRSPLIHGYWLKQFGIAGSYRAHEVTPEAFPEFMGQLRDGGTGFCGGNVTIP 73 Query: 72 FKERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLLGAIAIQAPGFDVTAAP 131 KE A ++D +L+ GAAN L + EDG + A NTDG G + + +A G+D + Sbjct: 74 HKEMAFELSDRPDELSAELGAANTL-WLEDGRICATNTDGRGFVANLDERASGWD-RIST 131 Query: 132 VVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALPALLPE 191 VILGAGGA+R + A+ G I VVNRT ARAQ+LAD FG V A AL ++ Sbjct: 132 AVILGAGGASRAVIQAVRDRGVKTIHVVNRTAARAQELADRFGRAVHAHPIAALSEVMAG 191 Query: 192 AGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTVDGLEM 251 AGL +N TSLG+ G P+ D + AVV D+VY PL+T LR+AE G R VDGL M Sbjct: 192 AGLFVNTTSLGMDGEPAPAIDFSPLANGAVVTDIVYVPLKTPLLRQAEEQGYRIVDGLGM 251 Query: 252 LLRQAIPTFETIYGQAPSPKIDVRVLALK 280 LL QA P FE +G P +R + +K Sbjct: 252 LLHQAAPGFEKWFGLRPVVDETLRQIIIK 280 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: 221 Number of extensions: 16 Number of successful extensions: 4 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: 286 Length adjustment: 26 Effective length of query: 259 Effective length of database: 260 Effective search space: 67340 Effective search space used: 67340 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_002827835.1 NGR_c33520 (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.4350.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-72 228.9 0.0 4e-72 228.6 0.0 1.0 1 lcl|NCBI__GCF_000018545.1:YP_002827835.1 NGR_c33520 shikimate 5-dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000018545.1:YP_002827835.1 NGR_c33520 shikimate 5-dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 228.6 0.0 4e-72 4e-72 5 266 .. 14 278 .. 11 282 .. 0.94 Alignments for each domain: == domain 1 score: 228.6 bits; conditional E-value: 4e-72 TIGR00507 5 viGnpikhSksplihnaalkqlgleleYlafeveieelekalsgika..lglkGvnvTvPfKeevlell 71 v G+pikhS splih lkq+g+++ Y a+ev++e++++++ +++ g+ G nvT+P+Ke ++el lcl|NCBI__GCF_000018545.1:YP_002827835.1 14 VTGYPIKHSRSPLIHGYWLKQFGIAGSYRAHEVTPEAFPEFMGQLRDggTGFCGGNVTIPHKEMAFELS 82 78*******************************************98346799**************** PP TIGR00507 72 DeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlka 139 D+ +e +++ga NTl ledg++ + nTDg G+v++L + s +++i+GAGGa++av+ + + lcl|NCBI__GCF_000018545.1:YP_002827835.1 83 DRPDELSAELGAANTLWLEDGRICATNTDGRGFVANLDErASGWDRISTAVILGAGGASRAVIQAVRDR 151 *************************************99877777799*******************99 PP TIGR00507 140 .dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellkeg 207 k++ ++NRt ++a+ela+r+ + + + + l +n+ts+g+ ge ++++ + l++g lcl|NCBI__GCF_000018545.1:YP_002827835.1 152 gVKTIHVVNRTAARAQELADRFGRAVHAHPIAALSEVMAGAGLFVNTTSLGMDGEP-APAIDFSPLANG 219 56899*******************8888878777788888**************98.9*********** PP TIGR00507 208 klvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealk 266 ++v D+vy pl+tpll+ a+++g +++dGlgMl +Qaa Fe+w+g p v+++ ++++ lcl|NCBI__GCF_000018545.1:YP_002827835.1 220 AVVTDIVYVPLKTPLLRQAEEQGYRIVDGLGMLLHQAAPGFEKWFGLRPVVDETLRQII 278 *************************************************9998877664 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (286 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.31 // [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