Align aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (characterized)
to candidate WP_041938733.1 FRAAL_RS02610 aspartate-semialdehyde dehydrogenase
Query= BRENDA::Q8KQ27 (354 letters) >NCBI__GCF_000058485.1:WP_041938733.1 Length = 365 Score = 426 bits (1095), Expect = e-124 Identities = 222/348 (63%), Positives = 266/348 (76%), Gaps = 6/348 (1%) Query: 3 PVLALVGATGAVGTVMIDIINNRETVPWGEIRLIASARSAGKKLTVRGEELTVIELTAEA 62 P LA+VGATGAVGTVM+ ++ R + WGEIR +ASARSAG+ + VRG ++ V L+ E Sbjct: 10 PTLAVVGATGAVGTVMLSMLAERPDI-WGEIRPVASARSAGRTVRVRGADVAVQVLSPEV 68 Query: 63 FDGVDVAMFDVPDEISAEWAPVAAARGAVAVDNSGAFRMDDDVPLVVPEVNADKVGERPR 122 FDGVDVA+FDVPDE+SA+WAPVAAARGAVAVDNSGAFRMDDDVPLVVPEVNAD++ RPR Sbjct: 69 FDGVDVAVFDVPDEVSAQWAPVAAARGAVAVDNSGAFRMDDDVPLVVPEVNADQLAARPR 128 Query: 123 GIIANPNCTTLSMMAALGALHREFELKELVVASYQAVSGAGKEGVDRLYAELEAVAG-KP 181 GIIANPNCTTLSM+ ALGALHR F L+ + ASYQA SGAG+ G+D LY +L V G + Sbjct: 129 GIIANPNCTTLSMIVALGALHRAFGLESMFAASYQAASGAGQAGIDTLYNQLATVGGTRE 188 Query: 182 VGVSAGDVRKTLEAAGLSISDSPFPAPLAFNVVPSAGSYKGDGWYSEELKVRNESRKILG 241 +G +AGDVRK + GL PFPAPLA NVVP AGS + GW SEE KVRNESRKILG Sbjct: 189 LGQTAGDVRKAIGEDGL----GPFPAPLALNVVPWAGSLRDGGWSSEEFKVRNESRKILG 244 Query: 242 IPDLKVSATCVRVPVVTTHSLAVHATFAREVTVEEAHKVFEAQPTIVLVDDPENGVFPTP 301 +PDL+VSATCVRVPV+TTH++AVHA FAR VT +EA V A P + +VDDP G FPTP Sbjct: 245 LPDLRVSATCVRVPVITTHAVAVHARFARPVTGDEARAVLLAAPGVAVVDDPSAGEFPTP 304 Query: 302 AEVVGEDPTYVGRVRQALDFPNTLDFLRVRGQPAQGAAAEHLRDAETL 349 ++VVG DPT+VGR+RQ+ D P+ + +GAA L+ AE L Sbjct: 305 SDVVGTDPTWVGRIRQSPDDPHEIALFLCGDNLRKGAALNTLQIAELL 352 Lambda K H 0.316 0.133 0.381 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: 434 Number of extensions: 15 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: 354 Length of database: 365 Length adjustment: 29 Effective length of query: 325 Effective length of database: 336 Effective search space: 109200 Effective search space used: 109200 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_041938733.1 FRAAL_RS02610 (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.26187.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-113 364.9 0.0 2.3e-113 364.7 0.0 1.0 1 lcl|NCBI__GCF_000058485.1:WP_041938733.1 FRAAL_RS02610 aspartate-semialde Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000058485.1:WP_041938733.1 FRAAL_RS02610 aspartate-semialdehyde dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 364.7 0.0 2.3e-113 2.3e-113 2 338 .. 12 354 .. 11 355 .. 0.96 Alignments for each domain: == domain 1 score: 364.7 bits; conditional E-value: 2.3e-113 TIGR01296 2 vaivGatGavGqellkvLeernfpidklvllasersaGkkvkfkgkeleveeaekesfegidialfsaG 70 +a+vGatGavG ++l +L+er +++++as+rsaG+ v+++g ++ v+ ++ e+f+g+d+a+f lcl|NCBI__GCF_000058485.1:WP_041938733.1 12 LAVVGATGAVGTVMLSMLAERPDIWGEIRPVASARSAGRTVRVRGADVAVQVLSPEVFDGVDVAVFDVP 80 79******************************************************************* PP TIGR01296 71 gsvskefapkaakagviviDntsafrldedvPLvvpevnaeelkeakkkgiianPnCstiqlvvvLkpl 139 vs ++ap aa++g++ +Dn+ afr+d+dvPLvvpevna++l+ ++ +giianPnC+t++++v+L +l lcl|NCBI__GCF_000058485.1:WP_041938733.1 81 DEVSAQWAPVAAARGAVAVDNSGAFRMDDDVPLVVPEVNADQLAARP-RGIIANPNCTTLSMIVALGAL 148 ******************************************99888.********************* PP TIGR01296 140 kdeaklkrvvvstYqavsGaGkkgveeLknqtkavlegkekepeida.......lkakkfakqiafnai 201 +++++l+++ ++Yqa sGaG++g++ L+nq+ +v +++e + + f++++a n++ lcl|NCBI__GCF_000058485.1:WP_041938733.1 149 HRAFGLESMFAASYQAASGAGQAGIDTLYNQLATVGGTRELGQTAGDvrkaigeDGLGPFPAPLALNVV 217 ****************************************9877664344443333467********** PP TIGR01296 202 plidklkedGytkeelkllfetrkilgiedlkvsatcvrvPvftghsesvsiefekelsveevkelLke 270 p +++l++ G +ee k+++e+rkilg +dl+vsatcvrvPv+t+h+++v++ f+++++ +e++ +L lcl|NCBI__GCF_000058485.1:WP_041938733.1 218 PWAGSLRDGGWSSEEFKVRNESRKILGLPDLRVSATCVRVPVITTHAVAVHARFARPVTGDEARAVLLA 286 ********************************************************************* PP TIGR01296 271 apgvvviddpsenlyptPleavgkdevfvgrirkDlskekglalfvvaDnlrkGaalnavqiaellik 338 apgv+v+ddps ++ptP ++vg+d ++vgrir+ ++ + +alf+ +DnlrkGaaln++qiaell++ lcl|NCBI__GCF_000058485.1:WP_041938733.1 287 APGVAVVDDPSAGEFPTPSDVVGTDPTWVGRIRQSPDDPHEIALFLCGDNLRKGAALNTLQIAELLVA 354 *****************************************************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (339 nodes) Target sequences: 1 (365 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: 8.95 // [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