Align aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_013451120.1 CALNI_RS04980 aspartate-semialdehyde dehydrogenase
Query= metacyc::AT1G14810-MONOMER (375 letters) >NCBI__GCF_000183405.1:WP_013451120.1 Length = 341 Score = 348 bits (894), Expect = e-100 Identities = 175/336 (52%), Positives = 234/336 (69%), Gaps = 8/336 (2%) Query: 40 SLAVVGVTGAVGQEFLSVLSDRDFPYSSIKMLASKRSAGKRVAFDGHEYTVEELTADSFN 99 ++A+ G TGAVG+ FL +L +R+FP + +++LAS RS GK + F G +Y V+ELT DSF Sbjct: 13 NVAIAGATGAVGETFLQILEERNFPINELRLLASARSVGKTIKFKGEDYKVQELTHDSFK 72 Query: 100 GVDIALFSAGGSISKEFGPLAAEKGTIVVDNSSAFRMVDGVPLVIPEVNPEAMKGIKVGM 159 G+DIALFSAG S S EF P A + G +V+DNSSAFRM +PLV+PEVN A Sbjct: 73 GIDIALFSAGASRSLEFAPSAVKAGALVIDNSSAFRMEKDIPLVVPEVNAAA------AF 126 Query: 160 GKGALIANPNCSTIICLMAVTPLHHHAKVKRMVVSTYQAASGAGAAAMEELVQQTREVLE 219 +IANPNC+TII ++A+ PLH + K+KR+VVS+YQ++SGAGA AMEEL+ QTR + Sbjct: 127 DNNGIIANPNCTTIIMVVALKPLHDYGKIKRVVVSSYQSSSGAGAQAMEELLAQTRAWAK 186 Query: 220 GKPPTCNIFGQQYAFNLFSHNAPILDNGYNEEEMKLVKETRKIWNDTEVKVTATCIRVPV 279 G+P F Q FN+ H +NGY +EEMK+ ETRKI D +KVTATC+RVPV Sbjct: 187 GEPIKVEKFQHQLLFNVIPHIDKFTENGYTKEEMKMFNETRKIMGDDTIKVTATCVRVPV 246 Query: 280 MRAHAESVNLQFENPLDENTAREILKKAPGVYIIDDRASNTFPTPLDVSNKDDVAVGRIR 339 + AH+E+V ++ E + ARE+L KAPGV ++D+ N +P PL V+ KDD VGRIR Sbjct: 247 ISAHSEAVTIETEKKITAEKARELLSKAPGVQVLDNPEKNEYPMPLFVAGKDDCYVGRIR 306 Query: 340 RDVSQDGNFGLDIFVCGDQIRKGAALNAVQIAEMLL 375 D++ D GL +V GDQ+RKGAALNA+QIAE+ + Sbjct: 307 EDITCDN--GLTFWVVGDQLRKGAALNAIQIAELFI 340 Lambda K H 0.318 0.133 0.380 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: 334 Number of extensions: 6 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: 375 Length of database: 341 Length adjustment: 29 Effective length of query: 346 Effective length of database: 312 Effective search space: 107952 Effective search space used: 107952 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_013451120.1 CALNI_RS04980 (aspartate-semialdehyde dehydrogenase)
to HMM TIGR01296 (asd: aspartate-semialdehyde dehydrogenase (EC 1.2.1.11))
# 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/TIGR01296.hmm # target sequence database: /tmp/gapView.8665.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01296 [M=339] Accession: TIGR01296 Description: asd_B: aspartate-semialdehyde 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-151 489.0 0.6 3.9e-151 488.9 0.6 1.0 1 lcl|NCBI__GCF_000183405.1:WP_013451120.1 CALNI_RS04980 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183405.1:WP_013451120.1 CALNI_RS04980 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 488.9 0.6 3.9e-151 3.9e-151 1 338 [. 13 341 .] 13 341 .] 0.99 Alignments for each domain: == domain 1 score: 488.9 bits; conditional E-value: 3.9e-151 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 nvai GatGavG+++l++Leernfpi++l+llas+rs Gk +kfkg++++v+e+++ sf+gidialfsa lcl|NCBI__GCF_000183405.1:WP_013451120.1 13 NVAIAGATGAVGETFLQILEERNFPINELRLLASARSVGKTIKFKGEDYKVQELTHDSFKGIDIALFSA 81 79******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 G+s s efap+a+kag++viDn+safr+++d+PLvvpevna+ ++ + giianPnC+ti +vv+Lkp lcl|NCBI__GCF_000183405.1:WP_013451120.1 82 GASRSLEFAPSAVKAGALVIDNSSAFRMEKDIPLVVPEVNAAAAFDNN--GIIANPNCTTIIMVVALKP 148 ********************************************9999..******************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+d k+krvvvs+Yq+ sGaG++++eeL qt+a+ +g+ +++ +kf++q+ fn+ip+idk+ lcl|NCBI__GCF_000183405.1:WP_013451120.1 149 LHDYGKIKRVVVSSYQSSSGAGAQAMEELLAQTRAWAKGEPIKV-------EKFQHQLLFNVIPHIDKF 210 ************************************99987665.......9***************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +e+Gytkee+k+ +etrki+g++ +kv+atcvrvPv+ +hse+v+ie+ek++++e+++elL +apgv+v lcl|NCBI__GCF_000183405.1:WP_013451120.1 211 TENGYTKEEMKMFNETRKIMGDDTIKVTATCVRVPVISAHSEAVTIETEKKITAEKARELLSKAPGVQV 279 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 +d+p++n+yp+Pl ++gkd+ +vgrir+D++ ++gl+ +vv+D+lrkGaalna+qiael+ik lcl|NCBI__GCF_000183405.1:WP_013451120.1 280 LDNPEKNEYPMPLFVAGKDDCYVGRIREDITCDNGLTFWVVGDQLRKGAALNAIQIAELFIK 341 **********************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (341 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: 00:00:00.01 # Mc/sec: 7.52 // [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