Align aspartate semialdehyde dehydrogenase subunit (EC 1.2.1.11) (characterized)
to candidate WP_092482508.1 BM299_RS05750 aspartate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-6564 (346 letters) >NCBI__GCF_900115975.1:WP_092482508.1 Length = 339 Score = 331 bits (849), Expect = 1e-95 Identities = 174/336 (51%), Positives = 233/336 (69%), Gaps = 9/336 (2%) Query: 7 VAVVGATGAVGQQMLKTLEDRNFEMDTLTLLSSKRSAGTKVTFKGQELTVQEASPESFEG 66 V +VGATGAVGQ++L+ L +RNF + L L ++ RSAG ++ FKG+ TV+E +P SF+G Sbjct: 6 VVIVGATGAVGQEILQVLAERNFPVGELKLCATARSAGKEIFFKGKSYTVEETTPASFDG 65 Query: 67 VNIALFSAGGSVSQALAPEAVKRGAIVIDNTSAFRMDENTPLVVPEVNEADLHEHNGIIA 126 ++IALF AGG+ S+ P A ++G +VIDN+S FR+D PLVVPEVN D+ EH GIIA Sbjct: 66 MDIALF-AGGAASKEFGPLAAEKGVVVIDNSSHFRLDPQVPLVVPEVNPEDVKEHRGIIA 124 Query: 127 NPNCSTIQMVAALEPIRKAYGLNKVIVSTYQAVSGAGNEAVKELYSQTQAILNKEEIEPE 186 NPNCSTI MV L+ I A G+ +V+VSTYQAVSGAG E + EL T+A+L+ +E+ P Sbjct: 125 NPNCSTIIMVVPLKAIYDAAGIKRVVVSTYQAVSGAGAEGITELTEHTRAVLDGKEVIPA 184 Query: 187 IMPVKGDKKHYQIAFNAIPQIDKFQDNGYTFEEMKMINETKKIMHMPDLQVAATCVRLPI 246 K YQIAFN IP ID FQ+ YT EE KM+ ET+KI+H + + AT VR+P+ Sbjct: 185 -------KFQYQIAFNLIPHIDVFQEMDYTKEEWKMVKETRKILHDDTVGITATTVRVPV 237 Query: 247 QTGHSESVYIEIDRDDATVEDIKNLLKEAPGVTLQDDPSQQLYPMPADAVGKNDVFVGRI 306 HSES+ +E R TV++ K +L + PGV ++DDP+ + YPMP K+DVFVGRI Sbjct: 238 YRSHSESINVETKR-KITVDEAKKVLADFPGVVVEDDPANKKYPMPLFTSEKDDVFVGRI 296 Query: 307 RKDLDRANGFHLWVVSDNLLKGAAWNSVQIAESLKK 342 R+D N ++WVV+D L KGAA N+VQIAE + K Sbjct: 297 RQDNSLDNALNMWVVADQLRKGAATNAVQIAELVIK 332 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: 322 Number of extensions: 12 Number of successful extensions: 4 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: 339 Length adjustment: 29 Effective length of query: 317 Effective length of database: 310 Effective search space: 98270 Effective search space used: 98270 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_092482508.1 BM299_RS05750 (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.8990.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-143 463.9 1.3 1.7e-143 463.7 1.3 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092482508.1 BM299_RS05750 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092482508.1 BM299_RS05750 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.7 1.3 1.7e-143 1.7e-143 2 338 .. 6 332 .. 5 333 .. 0.99 Alignments for each domain: == domain 1 score: 463.7 bits; conditional E-value: 1.7e-143 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 v ivGatGavGqe+l+vL+ernfp+ +l+l a +rsaGk++ fkgk ++vee++ +sf+g+dialf aG lcl|NCBI__GCF_900115975.1:WP_092482508.1 6 VVIVGATGAVGQEILQVLAERNFPVGELKLCATARSAGKEIFFKGKSYTVEETTPASFDGMDIALF-AG 73 89****************************************************************.79 PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 g+ skef p aa++gv+viDn+s frld++vPLvvpevn e++ke++ giianPnCsti +vv Lk++ lcl|NCBI__GCF_900115975.1:WP_092482508.1 74 GAASKEFGPLAAEKGVVVIDNSSHFRLDPQVPLVVPEVNPEDVKEHR--GIIANPNCSTIIMVVPLKAI 140 999*******************************************9..******************** PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeidalkakkfakqiafnaiplidklk 208 +d+a++krvvvstYqavsGaG++g+ eL+++t+avl+gke p kf++qiafn+ip+id ++ lcl|NCBI__GCF_900115975.1:WP_092482508.1 141 YDAAGIKRVVVSTYQAVSGAGAEGITELTEHTRAVLDGKEVIP-------AKFQYQIAFNLIPHIDVFQ 202 ****************************************997.......9****************** PP TIGR01296 209 edGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvvi 277 e ytkee k++ etrkil+++ + ++at+vrvPv+++hses+++e++++++v+e+k++L + pgvvv lcl|NCBI__GCF_900115975.1:WP_092482508.1 203 EMDYTKEEWKMVKETRKILHDDTVGITATTVRVPVYRSHSESINVETKRKITVDEAKKVLADFPGVVVE 271 ********************************************************************* PP TIGR01296 278 ddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 ddp +++yp+Pl +++kd+vfvgrir+D s +++l+++vvaD+lrkGaa+navqiael+ik lcl|NCBI__GCF_900115975.1:WP_092482508.1 272 DDPANKKYPMPLFTSEKDDVFVGRIRQDNSLDNALNMWVVADQLRKGAATNAVQIAELVIK 332 *********************************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (339 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: 7.81 // [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