Align shikimate dehydrogenase (EC 1.1.1.25) (characterized)
to candidate WP_015927972.1 MNOD_RS06165 shikimate dehydrogenase
Query= reanno::Caulo:CCNA_00003 (285 letters) >NCBI__GCF_000022085.1:WP_015927972.1 Length = 290 Score = 188 bits (477), Expect = 1e-52 Identities = 114/273 (41%), Positives = 139/273 (50%), Gaps = 8/273 (2%) Query: 14 VCGQPIKHSMSPVIHNAWIAAAGLDAAYVPFAPAADRFETFVDGLRGGAVRGLNVTIPFK 73 V G PI HS SP+IH W++A GL +Y A + F F+ G G NVTIP K Sbjct: 12 VVGHPIAHSRSPLIHGHWLSAHGLAGSYERLDVAPEAFADFLSGFPASGFVGGNVTIPHK 71 Query: 74 ERALAVADTASDLARMAGAANLLVFNEDGSVHADNTDGPGLL-------GAIAIQAPGFD 126 E A + T + A GA N L + G +H DNTD PG L GA + G Sbjct: 72 EAAFRLVATMTPRAERIGAVNTLSLDAAGRLHGDNTDAPGFLAHLDATLGADWPETTGIG 131 Query: 127 VTAAPVVILGAGGAARGAVAALLLAGAPRIAVVNRTVARAQDLADTFGEKVVAKGEDALP 186 ++LGAGGAAR LL G P I + NRT ARA+ L +V A D +P Sbjct: 132 A-GRTALLLGAGGAARAIAVGLLERGLPHIRIANRTAARAEALRGLDSARVEAVAWDHVP 190 Query: 187 ALLPEAGLIINATSLGLGGGAGPSADLTLTPKTAVVMDMVYKPLRTEFLRRAEAAGRRTV 246 LL EAGL++N TSLG+ G DL P A V D+VY PL T L A A RTV Sbjct: 191 GLLGEAGLLVNTTSLGMAGAEALDLDLAGLPDGAAVADIVYVPLETPLLAAARARSLRTV 250 Query: 247 DGLEMLLRQAIPTFETIYGQAPSPKIDVRVLAL 279 DGL MLL QA+P F +G P D+R L + Sbjct: 251 DGLGMLLHQAVPGFARWFGVTPQVTPDLRALVV 283 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: 255 Number of extensions: 11 Number of successful extensions: 2 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: 290 Length adjustment: 26 Effective length of query: 259 Effective length of database: 264 Effective search space: 68376 Effective search space used: 68376 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_015927972.1 MNOD_RS06165 (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.2324.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-67 212.3 0.0 4.7e-67 212.0 0.0 1.0 1 lcl|NCBI__GCF_000022085.1:WP_015927972.1 MNOD_RS06165 shikimate dehydroge Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000022085.1:WP_015927972.1 MNOD_RS06165 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 212.0 0.0 4.7e-67 4.7e-67 5 260 .. 12 276 .. 9 284 .. 0.91 Alignments for each domain: == domain 1 score: 212.0 bits; conditional E-value: 4.7e-67 TIGR00507 5 viGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlellDe 73 v+G+pi+hS splih + l+ gl++ Y +++v +e++ ++lsg+ a g+ G nvT+P+Ke++++l+ lcl|NCBI__GCF_000022085.1:WP_015927972.1 12 VVGHPIAHSRSPLIHGHWLSAHGLAGSYERLDVAPEAFADFLSGFPASGFVGGNVTIPHKEAAFRLVAT 80 89******************************************************************* PP TIGR00507 74 ieesakligavNTlkle.dgklvgynTDgiGlvssLek.l.......sklksekrvliiGAGGaakava 133 ++++a+ igavNTl l+ g+l g+nTD+ G+++ L l + + +++++l++GAGGaa+a+a lcl|NCBI__GCF_000022085.1:WP_015927972.1 81 MTPRAERIGAVNTLSLDaAGRLHGDNTDAPGFLAHLDAtLgadwpetTGIGAGRTALLLGAGGAARAIA 149 ***************76379****************976533222223467899*************** PP TIGR00507 134 leLlkadk.eviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevka 201 + Ll+ + ++ iaNRt ++ae+l + e +a++ l + l++n+ts+g+ g ++ lcl|NCBI__GCF_000022085.1:WP_015927972.1 150 VGLLERGLpHIRIANRTAARAEALRGLDSARVEAVAWDHVPGLLGEAGLLVNTTSLGMAGAE-ALDLDL 217 ****996438***********9999888887778888766666778**************98.788999 PP TIGR00507 202 ellkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvek 260 l g++v D+vy pletpll+ a+ + +++dGlgMl +Qa+ F w+gv p+v lcl|NCBI__GCF_000022085.1:WP_015927972.1 218 AGLPDGAAVADIVYVPLETPLLAAARARSLRTVDGLGMLLHQAVPGFARWFGVTPQVTP 276 99****************************************************99875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (290 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: 11.27 // [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