Align Shikimate dehydrogenase (NADP(+)); SDH; EC 1.1.1.25 (characterized)
to candidate WP_009562611.1 AFE_RS00850 shikimate dehydrogenase
Query= SwissProt::Q5KWX7 (276 letters) >NCBI__GCF_000021485.1:WP_009562611.1 Length = 298 Score = 167 bits (424), Expect = 2e-46 Identities = 107/272 (39%), Positives = 149/272 (54%), Gaps = 9/272 (3%) Query: 4 VYGLIGFPVEHSLSPLMHNDAFARLGIPARYHLFSVEPGQVGAAIAGVRALGIAGVNVTI 63 VYG++GFPV HSLSP +H A+ + Y F V + A+AG+ ALGI GVNVT+ Sbjct: 20 VYGILGFPVNHSLSPWLHRLFAAQQELDLVYVPFPVREEDIAVALAGLPALGIRGVNVTV 79 Query: 64 PHKLAVIPFLDEVDEHARRIGAVNTIINNDGRLVGYNTDGLGYVQALEEEMNITLDGKR- 122 PHK AV+P + + A IGAVNTI + G+NTD G+++ALE T DG R Sbjct: 80 PHKEAVLPLMQWLSAEALAIGAVNTICFTPSGMQGHNTDAPGFLRALE---RATGDGWRQ 136 Query: 123 --ILVIGAGGGARGIYFSLLSTAAERIDMANRTVEKAERLVRE--GDERRSAYFSLAEAE 178 VIGAGG AR I ++L I +ANR + +AE L + G A Sbjct: 137 CPATVIGAGGAARAIVYALGHAGCPAIYLANRHLPRAEVLAAQFPGLPVHPIPLDRAALS 196 Query: 179 TRLAEYDIIINTTSVGMHPRVEVQPLSLERLRPGVIVSDIIYNPLETKWLKEAKARGARV 238 L +++NT++ G+H + L L R+ V DI+YNPLET L+ A+ G Sbjct: 197 AVLPRSRLLVNTSTRGLHGEGHPE-LDLARMPGNGSVYDIVYNPLETPLLQAARQAGLGA 255 Query: 239 QNGVGMLVYQGALAFEKWTGQWPDVNRMKQLV 270 +G+GMLV QGA +F WTG P +++++ Sbjct: 256 VDGLGMLVEQGAESFRIWTGTLPQTAAVEEIL 287 Lambda K H 0.320 0.138 0.400 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: 259 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: 276 Length of database: 298 Length adjustment: 26 Effective length of query: 250 Effective length of database: 272 Effective search space: 68000 Effective search space used: 68000 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_009562611.1 AFE_RS00850 (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.20150.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 4.3e-67 212.1 0.0 1.0 1 lcl|NCBI__GCF_000021485.1:WP_009562611.1 AFE_RS00850 shikimate dehydrogen Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021485.1:WP_009562611.1 AFE_RS00850 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 212.1 0.0 4.3e-67 4.3e-67 2 269 .. 20 291 .. 19 292 .. 0.93 Alignments for each domain: == domain 1 score: 212.1 bits; conditional E-value: 4.3e-67 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 ++g++G p++hS+sp +h +++q++l+l+Y+ f+v++e++ al g+ alg++GvnvTvP+Ke+vl+l lcl|NCBI__GCF_000021485.1:WP_009562611.1 20 VYGILGFPVNHSLSPWLHRLFAAQQELDLVYVPFPVREEDIAVALAGLPALGIRGVNVTVPHKEAVLPL 88 79******************************************************************* PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlk 138 + ++ +a +igavNT+ + g+nTD+ G++ +Le+ + + +iGAGGaa+a++ +L + lcl|NCBI__GCF_000021485.1:WP_009562611.1 89 MQWLSAEALAIGAVNTICFTPSGMQGHNTDAPGFLRALERaTGDGWRQCPATVIGAGGAARAIVYALGH 157 ****************************************76665558899****************** PP TIGR00507 139 adk.eviiaNRtvekaeelaerlqelgeilalsleevelkk....vdliinatsaglsgeideaevkae 202 a++ ++ +aNR + +ae la +++ + ++l++ l+ l++n+ gl+ge ++e++ lcl|NCBI__GCF_000021485.1:WP_009562611.1 158 AGCpAIYLANRHLPRAEVLAAQFPG-LPVHPIPLDRAALSAvlprSRLLVNTSTRGLHGEG-HPELDLA 224 *985799****************99.345556666665555323378*************9.9****** PP TIGR00507 203 llkegklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 ++ + v+D+vynpletpll+ a++ g +dGlgMlv+Q+a sF++wtg++p+ v e+l++ l lcl|NCBI__GCF_000021485.1:WP_009562611.1 225 RMPGNGSVYDIVYNPLETPLLQAARQAGLGAVDGLGMLVEQGAESFRIWTGTLPQTAAVEEILRRWL 291 ********************************************************99999988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (298 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: 00:00:00.01 # Mc/sec: 7.73 // [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