Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_027721936.1 H589_RS0110325 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_000425265.1:WP_027721936.1 Length = 342 Score = 361 bits (927), Expect = e-104 Identities = 189/340 (55%), Positives = 240/340 (70%), Gaps = 8/340 (2%) Query: 7 VAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFEG 66 VAVVGATGAVG++MLK LE RNF + SS RSAGTKV +K +ELTV E +SFEG Sbjct: 8 VAVVGATGAVGREMLKVLEQRNFPASEVVPFSSSRSAGTKVPYKDEELTVIELKEDSFEG 67 Query: 67 VNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGIIA 126 +IALFSAGGS S+ AP A K G +V+DN+SA+RMD PLVVPEVN DL H GIIA Sbjct: 68 FDIALFSAGGSTSEKFAPLAAKAGCVVVDNSSAWRMDPKVPLVVPEVNPEDLDWHPGIIA 127 Query: 127 NPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIEPE 186 NPNCSTIQMV AL+PI A + ++IVSTYQAVSG G +A+ EL +Q + N ++ + Sbjct: 128 NPNCSTIQMVVALKPIHDAAKIKRIIVSTYQAVSGTGQKAITELETQVSRLFNNRDVVAD 187 Query: 187 IMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRLPI 246 + P +QIAFN +P ID F DNGYT EEMKM+NET+KIM ++V AT VR+P+ Sbjct: 188 VYP-------HQIAFNCLPHIDVFMDNGYTKEEMKMVNETRKIMGDDSIKVTATAVRVPV 240 Query: 247 QTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVGRI 306 HSESV IE + + TVE+ +N+L PG+T+ D P + YPM D G++DV+VGRI Sbjct: 241 FYSHSESVNIETE-EKVTVEECRNMLANFPGITVIDFPEKHHYPMAIDCAGEDDVYVGRI 299 Query: 307 RKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346 R+D NG ++W+VSDN+ KGAA N+VQIAE+L +LV Sbjct: 300 REDETIENGLNMWIVSDNIRKGAALNTVQIAETLIARDLV 339 Lambda K H 0.314 0.131 0.366 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: 335 Number of extensions: 10 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: 346 Length of database: 342 Length adjustment: 29 Effective length of query: 317 Effective length of database: 313 Effective search space: 99221 Effective search space used: 99221 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: 42 (22.0 bits) S2: 49 (23.5 bits)
Align candidate WP_027721936.1 H589_RS0110325 (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.15541.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-151 489.3 0.7 3.4e-151 489.1 0.7 1.0 1 lcl|NCBI__GCF_000425265.1:WP_027721936.1 H589_RS0110325 aspartate-semiald Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000425265.1:WP_027721936.1 H589_RS0110325 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 489.1 0.7 3.4e-151 3.4e-151 1 338 [. 7 335 .. 7 336 .. 0.99 Alignments for each domain: == domain 1 score: 489.1 bits; conditional E-value: 3.4e-151 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 +va+vGatGavG+e+lkvLe+rnfp++++v+++s+rsaG+kv +k++el+v e+++ sfeg dialfsa lcl|NCBI__GCF_000425265.1:WP_027721936.1 7 RVAVVGATGAVGREMLKVLEQRNFPASEVVPFSSSRSAGTKVPYKDEELTVIELKEDSFEGFDIALFSA 75 69******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Ggs+s++fap aakag++v+Dn+sa+r+d++vPLvvpevn e+l ++ giianPnCstiq+vv+Lkp lcl|NCBI__GCF_000425265.1:WP_027721936.1 76 GGSTSEKFAPLAAKAGCVVVDNSSAWRMDPKVPLVVPEVNPEDLDWHP--GIIANPNCSTIQMVVALKP 142 *********************************************999..******************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 ++d+ak+kr++vstYqavsG+G+k++ eL+ q+ ++ ++ a+ +++qiafn +p+id + lcl|NCBI__GCF_000425265.1:WP_027721936.1 143 IHDAAKIKRIIVSTYQAVSGTGQKAITELETQVSRLFNNRDVV-------ADVYPHQIAFNCLPHIDVF 204 ********************************99998887765.......79***************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +++Gytkee+k+++etrki+g++ +kv+at+vrvPvf++hsesv+ie+e++++vee +++L + pg++v lcl|NCBI__GCF_000425265.1:WP_027721936.1 205 MDNGYTKEEMKMVNETRKIMGDDSIKVTATAVRVPVFYSHSESVNIETEEKVTVEECRNMLANFPGITV 273 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 id p+++ yp+ ++ +g+d+v+vgrir+D + e+gl++++v+Dn+rkGaaln+vqiae+li+ lcl|NCBI__GCF_000425265.1:WP_027721936.1 274 IDFPEKHHYPMAIDCAGEDDVYVGRIREDETIENGLNMWIVSDNIRKGAALNTVQIAETLIA 335 ***********************************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (342 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: 9.45 // [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