Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_052664753.1 NITAL_RS03505 aspartate-semialdehyde dehydrogenase
Query= BRENDA::P9WNX5 (345 letters) >NCBI__GCF_000969705.1:WP_052664753.1 Length = 352 Score = 281 bits (719), Expect = 2e-80 Identities = 171/355 (48%), Positives = 216/355 (60%), Gaps = 17/355 (4%) Query: 1 MGLSIGIVGATGQVGQVMRTLLDERDFPASAVR-FFASARSQGRKLAFRGQEIEVEDAET 59 MG+ I +VGATG VG+ +R LL RD ASARS G KLA+R E+EV + Sbjct: 1 MGIKIAVVGATGAVGREVRHLLATRDIDIEGDPVLLASARSAGTKLAWRDGEVEVREVSE 60 Query: 60 ADPSGLDIALFSAGSAMSKVQAPRFAAAGVTVIDNSSAWRKDPDVPLVVSEVNFERDAHR 119 +G+DIA+FSAG A SK P AA G V+DNSSA+R D DVPLVVSEVN E Sbjct: 61 DAFAGVDIAIFSAGGARSKEWGPIAAAQGAVVVDNSSAFRMDDDVPLVVSEVNPEA-LRT 119 Query: 120 RPKGIIANPNCTTMAAMPVLKVLHDEARLVRLVVSSYQAVSGSGLAGVAELAEQARAVIG 179 RPKGI+ANPNCTTM M +K LHD L +V +SYQA G+G AG+ EL EQ+ ++G Sbjct: 120 RPKGIVANPNCTTMVLMVAVKPLHDAFGLTDVVATSYQAAGGAGQAGIRELLEQSAKLVG 179 Query: 180 GAEQLVYDGGALEFP-PPNTYVAPIAFNVVPLAGSLVDDGSGETDEDQKLRFESRKILGI 238 E+L G E T+ IAFN +P G+ DD TDE+ KL ESRKILG+ Sbjct: 180 DEERLRSRGLEAEAAVEAETFSKAIAFNTLPHCGNFADD--RYTDEEWKLVNESRKILGL 237 Query: 239 PDLLVSGTCVRVPVFTGHSLSINAEFAQPLSPERARELLDGATGVQLVD----------V 288 P L VS TCVRVPV GH ++ FA+P++ + L+GA G+ + D Sbjct: 238 PALRVSPTCVRVPVVVGHGIAARLSFAEPVTRDGLMAALEGAPGLVIEDGTGQDGEALAY 297 Query: 289 PTPLAAAGVDESLVGRIRRDPGVPDGRGLALFVSGDNLRKGAALNTIQIAELLTA 343 P+ L +AG DE +VGR+R D + D LFV+GDNL KGAALN +Q+AEL+ A Sbjct: 298 PSTLGSAGRDEVIVGRVRED--LADPHSANLFVAGDNLLKGAALNAVQLAELIAA 350 Lambda K H 0.317 0.135 0.382 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: 359 Number of extensions: 21 Number of successful extensions: 7 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: 345 Length of database: 352 Length adjustment: 29 Effective length of query: 316 Effective length of database: 323 Effective search space: 102068 Effective search space used: 102068 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: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_052664753.1 NITAL_RS03505 (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.9865.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-117 376.9 0.0 4.8e-117 376.8 0.0 1.0 1 lcl|NCBI__GCF_000969705.1:WP_052664753.1 NITAL_RS03505 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000969705.1:WP_052664753.1 NITAL_RS03505 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 376.8 0.0 4.8e-117 4.8e-117 1 336 [. 4 348 .. 4 351 .. 0.95 Alignments for each domain: == domain 1 score: 376.8 bits; conditional E-value: 4.8e-117 TIGR01296 1 nvaivGatGavGqellkvLeernfpid.klvllasersaGkkvkfkgkeleveeaekesfegidialfs 68 ++a+vGatGavG+e++++L+ r+ +i+ + vllas+rsaG+k++ ++ e+ev+e+++ f g+dia+fs lcl|NCBI__GCF_000969705.1:WP_052664753.1 4 KIAVVGATGAVGREVRHLLATRDIDIEgDPVLLASARSAGTKLAWRDGEVEVREVSEDAFAGVDIAIFS 72 69************************846799************************************* PP TIGR01296 69 aGgsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLk 137 aGg+ ske+ p aa++g++v+Dn+safr+d+dvPLvv+evn e l+ ++ kgi+anPnC+t+ l+v++k lcl|NCBI__GCF_000969705.1:WP_052664753.1 73 AGGARSKEWGPIAAAQGAVVVDNSSAFRMDDDVPLVVSEVNPEALRTRP-KGIVANPNCTTMVLMVAVK 140 *********************************************9988.******************* PP TIGR01296 138 plkdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeida.....lkakkfakqiafnai 201 pl+d+++l vv +Yqa GaG++g+ eL +q ++ +e+ ++ ++a++f+k iafn + lcl|NCBI__GCF_000969705.1:WP_052664753.1 141 PLHDAFGLTDVVATSYQAAGGAGQAGIRELLEQSAKLVGDEERLRSRGLeaeaaVEAETFSKAIAFNTL 209 *********************************9999888888766554556779************** PP TIGR01296 202 plidklkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLke 270 p+ +++ +d yt+ee kl++e+rkilg + l+vs tcvrvPv++gh ++ + f+++++ + + L++ lcl|NCBI__GCF_000969705.1:WP_052664753.1 210 PHCGNFADDRYTDEEWKLVNESRKILGLPALRVSPTCVRVPVVVGHGIAARLSFAEPVTRDGLMAALEG 278 ********************************************************************* PP TIGR01296 271 apgvvvid....dpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiael 335 apg+v+ d d + +yp+ l +g+dev vgr+r+Dl + ++ +lfv++Dnl+kGaalnavq+ael lcl|NCBI__GCF_000969705.1:WP_052664753.1 279 APGLVIEDgtgqDGEALAYPSTLGSAGRDEVIVGRVREDLADPHSANLFVAGDNLLKGAALNAVQLAEL 347 *****9983333445679*************************************************98 PP TIGR01296 336 l 336 + lcl|NCBI__GCF_000969705.1:WP_052664753.1 348 I 348 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (352 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: 9.70 // [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