Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_069661975.1 BCR25_RS02295 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_001730305.1:WP_069661975.1 Length = 351 Score = 432 bits (1111), Expect = e-126 Identities = 216/344 (62%), Positives = 268/344 (77%), Gaps = 3/344 (0%) Query: 6 HVAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFE 65 +VAVVGATGAVG +M++ L + ++ + LL+SKRSAG + TFKGQ L ++E PESFE Sbjct: 6 NVAVVGATGAVGTKMIEMLAESTLPLNQVKLLASKRSAGKERTFKGQTLVIEELVPESFE 65 Query: 66 GVNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGII 125 G++IALFSAGGS+S+ APEAVKRGA+V+DNTS FRMD + PLVVPEVN L H GII Sbjct: 66 GIDIALFSAGGSISKQFAPEAVKRGAVVVDNTSHFRMDPDVPLVVPEVNPDALKRHKGII 125 Query: 126 ANPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILN---KEE 182 ANPNCSTIQ++ ALEPIRKAYGL+++IVSTYQAVSGAG A++EL +Q +N E+ Sbjct: 126 ANPNCSTIQLMVALEPIRKAYGLDRLIVSTYQAVSGAGIHAMEELKTQATEYINGTPAEK 185 Query: 183 IEPEIMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCV 242 + I+P GDKKHY IAFNA+PQID F D+ YT+EE KMINETKKIM ++V ATCV Sbjct: 186 LAANILPCGGDKKHYPIAFNALPQIDVFSDDDYTYEEWKMINETKKIMEDDGIKVVATCV 245 Query: 243 RLPIQTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVF 302 R+P+ +GHSESVYIE+ D A V IK L++ APG LQDDPSQQ+YP ++ + + F Sbjct: 246 RIPVLSGHSESVYIEVKEDGADVAKIKKLIETAPGAVLQDDPSQQVYPQALMSIDRKETF 305 Query: 303 VGRIRKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKKLNLV 346 VGRIRKD+D GFH+WVVSDNLLKGAAWNSVQIAE+L ++LV Sbjct: 306 VGRIRKDIDIEKGFHMWVVSDNLLKGAAWNSVQIAETLHAMDLV 349 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: 386 Number of extensions: 15 Number of successful extensions: 2 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: 351 Length adjustment: 29 Effective length of query: 317 Effective length of database: 322 Effective search space: 102074 Effective search space used: 102074 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_069661975.1 BCR25_RS02295 (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.3893397.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-144 466.3 0.2 3.2e-144 466.1 0.2 1.0 1 NCBI__GCF_001730305.1:WP_069661975.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001730305.1:WP_069661975.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.1 0.2 3.2e-144 3.2e-144 1 337 [. 6 344 .. 6 346 .. 0.96 Alignments for each domain: == domain 1 score: 466.1 bits; conditional E-value: 3.2e-144 TIGR01296 1 nvaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaGgsv 73 nva+vGatGavG +++++L+e++ p+++++llas+rsaGk+ +fkg+ l +ee+ esfegidialfsaGgs+ NCBI__GCF_001730305.1:WP_069661975.1 6 NVAVVGATGAVGTKMIEMLAESTLPLNQVKLLASKRSAGKERTFKGQTLVIEELVPESFEGIDIALFSAGGSI 78 79*********************************************************************** PP TIGR01296 74 skefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkplkdeaklk 146 sk+fap+a+k+g++v+Dnts fr+d+dvPLvvpevn + lk +k giianPnCstiql+v+L+p++++++l NCBI__GCF_001730305.1:WP_069661975.1 79 SKQFAPEAVKRGAVVVDNTSHFRMDPDVPLVVPEVNPDALKRHK--GIIANPNCSTIQLMVALEPIRKAYGLD 149 ****************************************9988..*************************** PP TIGR01296 147 rvvvstYqavsGaGkkgveeLknqtkavlegkekepeida...lkakkfakqiafnaiplidklkedGytkee 216 r++vstYqavsGaG +++eeLk q+ ++g+ e ++k++++iafna+p+id +++d yt ee NCBI__GCF_001730305.1:WP_069661975.1 150 RLIVSTYQAVSGAGIHAMEELKTQATEYINGTPAEKLAANilpCGGDKKHYPIAFNALPQIDVFSDDDYTYEE 222 *****************************98655433322234899*************************** PP TIGR01296 217 lkllfetrkilgiedlkvsatcvrvPvftghsesvsiefek.elsveevkelLkeapgvvviddpsenlyptP 288 k+++et+ki++++ +kv atcvr+Pv+ ghsesv+ie+++ ++v ++k+l++ apg v++ddps+++yp NCBI__GCF_001730305.1:WP_069661975.1 223 WKMINETKKIMEDDGIKVVATCVRIPVLSGHSESVYIEVKEdGADVAKIKKLIETAPGAVLQDDPSQQVYPQA 295 ***************************************88579***************************** PP TIGR01296 289 leavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 l+ ++ e+fvgrirkD++ ekg++++vv+Dnl+kGaa+n+vqiae+l NCBI__GCF_001730305.1:WP_069661975.1 296 LMSIDRKETFVGRIRKDIDIEKGFHMWVVSDNLLKGAAWNSVQIAETLH 344 **********************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (351 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: 00:00:00.00 # Mc/sec: 26.47 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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