Align shikimate dehydrogenase (NADP+) (EC 1.1.1.25) (characterized)
to candidate WP_050463258.1 AKL27_RS12890 shikimate dehydrogenase
Query= BRENDA::Q88RQ5 (274 letters) >NCBI__GCF_001189915.1:WP_050463258.1 Length = 277 Score = 281 bits (719), Expect = 1e-80 Identities = 157/274 (57%), Positives = 186/274 (67%), Gaps = 4/274 (1%) Query: 1 MDQYVVFGNPIGHSKSPLIHRLFAEQTGQDLEYATLLAPLDEFSDCARGFFKQGS-GGNV 59 MD YVV GNPI HSKSP IH FA QTGQ L Y LLAPL F+D R F QG G NV Sbjct: 1 MDAYVVIGNPIAHSKSPEIHAQFAAQTGQVLSYERLLAPLHGFADSVRTFIGQGGRGANV 60 Query: 60 TVPFKEEAFRLCDSLTPRARRAGAVNTLSKLADGTLQGDNTDGAGLVRDLTVNAGVELAG 119 T+PFK +A L LT RAR AGAVNTL + + GDNTDGAGLV D+ NAGV L G Sbjct: 61 TLPFKLDAHALATRLTERARLAGAVNTL-RFDGAEILGDNTDGAGLVADIVHNAGVALQG 119 Query: 120 KRILILGAGGAVRGVLEPILAHKPQSLVIANRTVEKAEQLAREFDELGPVVASGFAWLQE 179 KRIL++GAGGA RG L P+L +P LV+ NRT KA++LA +F G V A+ +A L Sbjct: 120 KRILLMGAGGASRGALLPLLEQRPGELVLVNRTAAKAQELAAQFTVYGNVAAAAYADLSG 179 Query: 180 PVDVIINATSASLAGELPPIADSLVEAGRTVCYDMMYGKEPTPFCQWATKLGAAKVLDGL 239 DV++NATSASL ++PP+ ++ + G T+ YDMMYG + T F Q+A + GA DGL Sbjct: 180 GFDVVVNATSASLDADVPPLPVAVFQPG-TLAYDMMYGAQDTVFMQFAQRHGAL-ARDGL 237 Query: 240 GMLAEQAAEAFFIWRGVRPDTAPVLAELRRQLAR 273 GML EQAAEAFF+WRGVRP T V A LRRQL R Sbjct: 238 GMLVEQAAEAFFLWRGVRPRTDEVFASLRRQLGR 271 Lambda K H 0.319 0.137 0.405 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: 238 Number of extensions: 11 Number of successful extensions: 5 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: 274 Length of database: 277 Length adjustment: 25 Effective length of query: 249 Effective length of database: 252 Effective search space: 62748 Effective search space used: 62748 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_050463258.1 AKL27_RS12890 (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.31310.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-79 252.9 0.0 1.7e-79 252.7 0.0 1.0 1 lcl|NCBI__GCF_001189915.1:WP_050463258.1 AKL27_RS12890 shikimate dehydrog Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001189915.1:WP_050463258.1 AKL27_RS12890 shikimate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 252.7 0.0 1.7e-79 1.7e-79 2 269 .. 3 269 .. 2 270 .. 0.96 Alignments for each domain: == domain 1 score: 252.7 bits; conditional E-value: 1.7e-79 TIGR00507 2 llgviGnpikhSksplihnaalkqlgleleYlafeveieelekalsgikalglkGvnvTvPfKeevlel 70 + viGnpi+hSksp ih ++++q+g+ l Y ++ ++++ + + + ++ +g +G+nvT+PfK + +l lcl|NCBI__GCF_001189915.1:WP_050463258.1 3 AYVVIGNPIAHSKSPEIHAQFAAQTGQVLSYERLLAPLHGFADSVRTFIGQGGRGANVTLPFKLDAHAL 71 588****************************************************************** PP TIGR00507 71 lDeieesakligavNTlkledgklvgynTDgiGlvssLek.lsklksekrvliiGAGGaakavaleLlk 138 + +++e+a+l+gavNTl+ ++ +++g+nTDg Glv+++ + ++kr+l++GAGGa+++++l+Ll+ lcl|NCBI__GCF_001189915.1:WP_050463258.1 72 ATRLTERARLAGAVNTLRFDGAEILGDNTDGAGLVADIVHnAGVALQGKRILLMGAGGASRGALLPLLE 140 **************************************997666667********************99 PP TIGR00507 139 a.dkeviiaNRtvekaeelaerlqelgeilalsleevelkkvdliinatsaglsgeideaevkaellke 206 + + e++++NRt +ka+ela ++ +g++ a +++ +d+++natsa+l ++ ++++ +++ lcl|NCBI__GCF_001189915.1:WP_050463258.1 141 QrPGELVLVNRTAAKAQELAAQFTVYGNVAAAAYADLSG-GFDVVVNATSASLDADV--PPLPVAVFQP 206 9899***************************99887754.6****************..9********* PP TIGR00507 207 gklvvDlvynpletpllkeakkkgtkvidGlgMlvaQaalsFelwtgvepdvekvfealkekl 269 g+l++D++y +t++++ a+++g+ dGlgMlv+Qaa +F lw+gv p ++vf l+++l lcl|NCBI__GCF_001189915.1:WP_050463258.1 207 GTLAYDMMYGAQDTVFMQFAQRHGALARDGLGMLVEQAAEAFFLWRGVRPRTDEVFASLRRQL 269 ********************************************************9999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (270 nodes) Target sequences: 1 (277 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: 00:00:00.01 # Mc/sec: 6.48 // [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