Align Aspartate-semialdehyde dehydrogenase 2; ASA dehydrogenase 2; ASADH 2; Aspartate-beta-semialdehyde dehydrogenase 2; EC 1.2.1.11 (characterized)
to candidate WP_011840132.1 RSPH17029_RS00225 aspartate-semialdehyde dehydrogenase
Query= SwissProt::P23247 (337 letters) >NCBI__GCF_000015985.1:WP_011840132.1 Length = 340 Score = 314 bits (805), Expect = 2e-90 Identities = 168/332 (50%), Positives = 229/332 (68%), Gaps = 6/332 (1%) Query: 5 FNVAIFGATGAVGETMLEVLQEREFPVDELFLLASERSEGKTYRFNGKTVRVQNVEEFDW 64 + V + GATG VG ML +L EREFPV+E+ LAS +S G F KT+ ++++ FD+ Sbjct: 3 YRVVVAGATGNVGREMLNILAEREFPVEEIAALASRKSLGTEVSFGDKTLTTKDLDTFDF 62 Query: 65 SQVHIALFSAGGELSAKWAPIAAEAGVVVIDNTSHFRYDYDIPLVVPEVNPEAIAEFRNR 124 + IALF+ G + + +AP AA AG VVIDN+S +RYD +PL+VPEVN +AI ++ + Sbjct: 63 TGWDIALFAVGSDATKIYAPKAAAAGCVVIDNSSLYRYDPQVPLIVPEVNADAIEGYKAK 122 Query: 125 NIIANPNCSTIQMLVALKPIYDAVGIERINVTTYQSVSGAGKAGIDELAGQTAKL-LNGY 183 NIIANPNCST QM+VALKP++D I+R+ V+TYQSVSGAGKAGIDEL QT + + G Sbjct: 123 NIIANPNCSTAQMVVALKPLHDRARIKRVVVSTYQSVSGAGKAGIDELWNQTKGIYVPGQ 182 Query: 184 PAETNTFSQQIAFNCIPQIDQFMDNGYTKEEMKMVWETQKIFNDPSIMVNPTCVRVPVFY 243 E + F++QIAFN IP ID FM++G TKEE KMV ET+KI DP + V TCVRVPVF Sbjct: 183 EVEPSKFTKQIAFNVIPHIDSFMEDGSTKEEWKMVAETKKIL-DPKVKVTATCVRVPVFV 241 Query: 244 GHAEAVHVETRAPIDAEQVMDMLEQTDG---IELFRGADFPTQVRDAGGKDHVLVGRVRN 300 GH+EA+++E +D E+ D+L + G ++ + T V + G+ + R+R Sbjct: 242 GHSEAINIEFEDFLDEEEARDILREAPGVLVVDKREAGGYITPV-ECVGEYATYISRIRQ 300 Query: 301 DISHHSGINLWVVADNVRKGAATNAVQIAELL 332 D + +G+NLW V+DN+RKGAA NAVQIAE+L Sbjct: 301 DSTLDNGLNLWCVSDNLRKGAALNAVQIAEVL 332 Lambda K H 0.319 0.135 0.395 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: 19 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: 337 Length of database: 340 Length adjustment: 28 Effective length of query: 309 Effective length of database: 312 Effective search space: 96408 Effective search space used: 96408 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_011840132.1 RSPH17029_RS00225 (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.14926.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-144 466.6 0.1 2.6e-144 466.4 0.1 1.0 1 lcl|NCBI__GCF_000015985.1:WP_011840132.1 RSPH17029_RS00225 aspartate-semi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015985.1:WP_011840132.1 RSPH17029_RS00225 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.4 0.1 2.6e-144 2.6e-144 2 337 .. 5 333 .. 4 335 .. 0.98 Alignments for each domain: == domain 1 score: 466.4 bits; conditional E-value: 2.6e-144 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 v + GatG+vG+e+l++L+er+fp++++ +las++s G++v f +k l+ +++++++f g dialf+ G lcl|NCBI__GCF_000015985.1:WP_011840132.1 5 VVVAGATGNVGREMLNILAEREFPVEEIAALASRKSLGTEVSFGDKTLTTKDLDTFDFTGWDIALFAVG 73 7899***************************************************************** PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 + k +apkaa+ag++viDn+s++r d++vPL+vpevna+ ++ k k+iianPnCst q+vv+Lkpl lcl|NCBI__GCF_000015985.1:WP_011840132.1 74 SDATKIYAPKAAAAGCVVIDNSSLYRYDPQVPLIVPEVNADAIEGYKAKNIIANPNCSTAQMVVALKPL 142 ********************************************************************* PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavle.gkekepeidalkakkfakqiafnaiplidkl 207 +d+a++krvvvstYq+vsGaGk+g++eL nqtk +++ g+e e ++kf+kqiafn+ip+id++ lcl|NCBI__GCF_000015985.1:WP_011840132.1 143 HDRARIKRVVVSTYQSVSGAGKAGIDELWNQTKGIYVpGQEVE-------PSKFTKQIAFNVIPHIDSF 204 **********************************987245555.......69***************** PP TIGR01296 208 kedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLkeapgvvv 276 +edG tkee k++ et+kil+ +++kv+atcvrvPvf+ghse+++iefe+ l+ ee++++L+eapgv v lcl|NCBI__GCF_000015985.1:WP_011840132.1 205 MEDGSTKEEWKMVAETKKILD-PKVKVTATCVRVPVFVGHSEAINIEFEDFLDEEEARDILREAPGVLV 272 *********************.*********************************************** PP TIGR01296 277 iddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaelli 337 +d+ + y+tP+e vg+ +++++rir+D + ++gl+l++v+DnlrkGaalnavqiae l lcl|NCBI__GCF_000015985.1:WP_011840132.1 273 VDKREAGGYITPVECVGEYATYISRIRQDSTLDNGLNLWCVSDNLRKGAALNAVQIAEVLG 333 **********************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (340 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: 9.75 // [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