Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_089323555.1 CHB58_RS07865 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_900188395.1:WP_089323555.1 Length = 337 Score = 388 bits (996), Expect = e-112 Identities = 204/341 (59%), Positives = 255/341 (74%), Gaps = 7/341 (2%) Query: 6 HVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFE 65 +VAVVGATGAVG++M+K LE+RNF + L LL+S RSAG K+ FKG+E+TV+E PESFE Sbjct: 4 NVAVVGATGAVGKEMIKILEERNFPVKNLKLLASARSAGKKLLFKGEEITVEELKPESFE 63 Query: 66 GVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGII 125 G++IALFSAGG S+ APEAVKRGA+VIDN+SAFRMD++ PLVVPEVN D+ H GII Sbjct: 64 GIDIALFSAGGDRSKQFAPEAVKRGAVVIDNSSAFRMDKDVPLVVPEVNPEDVKWHKGII 123 Query: 126 ANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIEP 185 ANPNCSTIQMV L+P+ + +V+VSTYQAVSGAG EA++EL QT AILN++E Sbjct: 124 ANPNCSTIQMVVVLKPLYDLSKIKRVVVSTYQAVSGAGAEAIEELKKQTGAILNEKE--- 180 Query: 186 EIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRLP 245 P K QIAFN +PQID F ++GYT EE KM+NETKKIMH ++V+ATCVR+P Sbjct: 181 ---PPAPHKIPKQIAFNCVPQIDVFFEDGYTKEEHKMVNETKKIMHDESIKVSATCVRVP 237 Query: 246 IQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVGR 305 + GHSESV +E ++ +VE LK+APGV++ DD +YP P D GK+DV VGR Sbjct: 238 VFIGHSESVNVEFEK-PVSVETAMEALKKAPGVSVVDDFKNGIYPTPVDVAGKDDVLVGR 296 Query: 306 IRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346 IRKD NG +LW+V DNL KGAA N+VQIAE L + NL+ Sbjct: 297 IRKDDTIDNGLNLWIVGDNLRKGAALNAVQIAEILIQENLI 337 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: 369 Number of extensions: 17 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: 337 Length adjustment: 29 Effective length of query: 317 Effective length of database: 308 Effective search space: 97636 Effective search space used: 97636 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_089323555.1 CHB58_RS07865 (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.13563.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-162 524.5 2.5 6.6e-162 524.3 2.5 1.0 1 lcl|NCBI__GCF_900188395.1:WP_089323555.1 CHB58_RS07865 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188395.1:WP_089323555.1 CHB58_RS07865 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 524.3 2.5 6.6e-162 6.6e-162 1 338 [. 4 333 .. 4 334 .. 0.99 Alignments for each domain: == domain 1 score: 524.3 bits; conditional E-value: 6.6e-162 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsa 69 nva+vGatGavG+e++k+Leernfp+++l+llas+rsaGkk+ fkg+e++vee++ esfegidialfsa lcl|NCBI__GCF_900188395.1:WP_089323555.1 4 NVAVVGATGAVGKEMIKILEERNFPVKNLKLLASARSAGKKLLFKGEEITVEELKPESFEGIDIALFSA 72 79******************************************************************* PP TIGR01296 70 GgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkp 138 Gg sk+fap+a+k+g++viDn+safr+d+dvPLvvpevn e++k +k giianPnCstiq+vvvLkp lcl|NCBI__GCF_900188395.1:WP_089323555.1 73 GGDRSKQFAPEAVKRGAVVIDNSSAFRMDKDVPLVVPEVNPEDVKWHK--GIIANPNCSTIQMVVVLKP 139 *********************************************998..******************* PP TIGR01296 139 lkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidkl 207 l+d k+krvvvstYqavsGaG++++eeLk+qt a+l+ ke ++k +kqiafn +p+id + lcl|NCBI__GCF_900188395.1:WP_089323555.1 140 LYDLSKIKRVVVSTYQAVSGAGAEAIEELKKQTGAILNEKEPP------APHKIPKQIAFNCVPQIDVF 202 *************************************988876......69****************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +edGytkee+k+++et+ki+++e +kvsatcvrvPvf+ghsesv++efek++sve + e Lk+apgv v lcl|NCBI__GCF_900188395.1:WP_089323555.1 203 FEDGYTKEEHKMVNETKKIMHDESIKVSATCVRVPVFIGHSESVNVEFEKPVSVETAMEALKKAPGVSV 271 ********************************************************************* PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 +dd ++ yptP++++gkd+v+vgrirkD + ++gl+l++v+DnlrkGaalnavqiae li+ lcl|NCBI__GCF_900188395.1:WP_089323555.1 272 VDDFKNGIYPTPVDVAGKDDVLVGRIRKDDTIDNGLNLWIVGDNLRKGAALNAVQIAEILIQ 333 ***********************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (337 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 6.39 // [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