Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate WP_067478856.1 BJL86_RS15630 aspartate ammonia-lyase
Query= BRENDA::P0AC38 (478 letters) >NCBI__GCF_001659785.1:WP_067478856.1 Length = 499 Score = 640 bits (1650), Expect = 0.0 Identities = 315/473 (66%), Positives = 379/473 (80%) Query: 6 RIEEDLLGTREVPADAYYGVHTLRAIENFYISNNKISDIPEFVRGMVMVKKAAAMANKEL 65 R+EEDLLG + VPA+AYYGVHT RAIENF IS I+DIP+F+RGMV VKKA A+AN+++ Sbjct: 20 RVEEDLLGEKAVPAEAYYGVHTARAIENFPISKLTINDIPDFIRGMVQVKKATALANRDM 79 Query: 66 QTIPKSVANAIIAACDEVLNNGKCMDQFPVDVYQGGAGTSVNMNTNEVLANIGLELMGHQ 125 + + AI+ ACD+VL+ G+CMDQFP +QGGAGTS+NMNTNEV+AN+ LE MG + Sbjct: 80 GVLTEEKCEAIVWACDQVLDEGRCMDQFPSCQFQGGAGTSINMNTNEVIANLALEHMGVE 139 Query: 126 KGEYQYLNPNDHVNKCQSTNDAYPTGFRIAVYSSLIKLVDAINQLREGFERKAVEFQDIL 185 KG Y ++PND VN+ QSTNDAYP+GFR+A++++L + A+ LRE F KA F+D+L Sbjct: 140 KGRYDVISPNDDVNRSQSTNDAYPSGFRLALWAALERYEKALIALREAFYDKAEAFRDVL 199 Query: 186 KMGRTQLQDAVPMTLGQEFRAFSILLKEEVKNIQRTAELLLEVNLGATAIGTGLNTPKEY 245 KMGRTQLQDAVPM+LGQE A+++ L EE+ + +A+ LL +NLGATAIGTG+NTP Y Sbjct: 200 KMGRTQLQDAVPMSLGQELGAYAVNLDEEMSVLASSAKTLLALNLGATAIGTGVNTPPHY 259 Query: 246 SPLAVKKLAEVTGFPCVPAEDLIEATSDCGAYVMVHGALKRLAVKMSKICNDLRLLSSGP 305 ++ L EVTG P AEDLIEAT D G YV+VH ALKR AVK+SKICNDLRLLSSGP Sbjct: 260 QESVIEHLKEVTGLPVSGAEDLIEATQDTGDYVLVHAALKRTAVKISKICNDLRLLSSGP 319 Query: 306 RAGLNEINLPELQAGSSIMPAKVNPVVPEVVNQVCFKVIGNDTTVTMAAEAGQLQLNVME 365 RAGLNEINLPE+QAGSSIMPAKVNPV+PEVVNQVCFKVIGND TV+ AAEAGQLQLNVME Sbjct: 320 RAGLNEINLPEMQAGSSIMPAKVNPVIPEVVNQVCFKVIGNDVTVSAAAEAGQLQLNVME 379 Query: 366 PVIGQAMFESVHILTNACYNLLEKCINGITANKEVCEGYVYNSIGIVTYLNPFIGHHNGD 425 P I Q+MFES+ +LTNACY L EKC+ GITAN+E+ +V NSIGIVTYLNP IGHHNGD Sbjct: 380 PAIAQSMFESIDLLTNACYTLAEKCVAGITANEEIARNFVMNSIGIVTYLNPIIGHHNGD 439 Query: 426 IVGKICAETGKSVREVVLERGLLTEAELDDIFSVQNLMHPAYKAKRYTDESEQ 478 +VGK CA +G+ VREVVLE GLL E ELDDI S QNL+HP +K RY D+ Q Sbjct: 440 LVGKECARSGRGVREVVLEMGLLDEEELDDILSPQNLLHPEFKGTRYLDKMRQ 492 Lambda K H 0.317 0.134 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: 654 Number of extensions: 13 Number of successful extensions: 1 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: 478 Length of database: 499 Length adjustment: 34 Effective length of query: 444 Effective length of database: 465 Effective search space: 206460 Effective search space used: 206460 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: 52 (24.6 bits)
Align candidate WP_067478856.1 BJL86_RS15630 (aspartate ammonia-lyase)
to HMM TIGR00839 (aspA: aspartate ammonia-lyase (EC 4.3.1.1))
# 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.carbon/TIGR00839.hmm # target sequence database: /tmp/gapView.1860874.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00839 [M=468] Accession: TIGR00839 Description: aspA: aspartate ammonia-lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-231 753.6 0.2 5.3e-231 753.4 0.2 1.0 1 NCBI__GCF_001659785.1:WP_067478856.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001659785.1:WP_067478856.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 753.4 0.2 5.3e-231 5.3e-231 1 467 [. 20 487 .. 20 488 .. 1.00 Alignments for each domain: == domain 1 score: 753.4 bits; conditional E-value: 5.3e-231 TIGR00839 1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaidekiakaiva 73 r+e+dllGek v+ae+yyG++t ra+enf+is+ +i+d+p+f++++v+vkka+alan +++ ++e+ +aiv NCBI__GCF_001659785.1:WP_067478856.1 20 RVEEDLLGEKAVPAEAYYGVHTARAIENFPISKLTINDIPDFIRGMVQVKKATALANRDMGVLTEEKCEAIVW 92 89*********************************************************************** PP TIGR00839 74 acdeile.GkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnpndhvnksqstndaypta 145 acd++l+ G+++dqf++ +qGGaGts+nmntnevianlale +G +kG y +++pnd vn+sqstndayp++ NCBI__GCF_001659785.1:WP_067478856.1 93 ACDQVLDeGRCMDQFPSCQFQGGAGTSINMNTNEVIANLALEHMGVEKGRYDVISPNDDVNRSQSTNDAYPSG 165 ******99***************************************************************** PP TIGR00839 146 lkiavyesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpltlGqefeayalllerdvkrikrtrel 218 +++a++ le+ +++ alr+af +ka+ f+dvlkmGrtqlqdavp+ lGqe+ aya+ l++++ + ++++ NCBI__GCF_001659785.1:WP_067478856.1 166 FRLALWAALERYEKALIALREAFYDKAEAFRDVLKMGRTQLQDAVPMSLGQELGAYAVNLDEEMSVLASSAKT 238 ************************************************************************* PP TIGR00839 219 llevnlGataiGtGlnadkeysklvvkklaevtGlplvpaenlieatsdtgayvevsgalkriavklskvcnd 291 ll +nlGataiGtG+n++++y++ v+ +l+evtGlp+ +ae+lieat+dtg yv v++alkr+avk+sk+cnd NCBI__GCF_001659785.1:WP_067478856.1 239 LLALNLGATAIGTGVNTPPHYQESVIEHLKEVTGLPVSGAEDLIEATQDTGDYVLVHAALKRTAVKISKICND 311 ************************************************************************* PP TIGR00839 292 lrllssGpraGlneinlpelqaGssimpakvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviaf 364 lrllssGpraGlneinlpe+qaGssimpakvnpv+pevvnqvcfkviGnd tv+ aaeaGqlqlnv+ep ia+ NCBI__GCF_001659785.1:WP_067478856.1 312 LRLLSSGPRAGLNEINLPEMQAGSSIMPAKVNPVIPEVVNQVCFKVIGNDVTVSAAAEAGQLQLNVMEPAIAQ 384 ************************************************************************* PP TIGR00839 365 allesisiltnaiesltdkcveGitanekicedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvl 437 +++esi++ltna+++l +kcv Gitane+i +++v+nsiGivt+lnp iG+++++lv+ke++++g++vr+vvl NCBI__GCF_001659785.1:WP_067478856.1 385 SMFESIDLLTNACYTLAEKCVAGITANEEIARNFVMNSIGIVTYLNPIIGHHNGDLVGKECARSGRGVREVVL 457 ************************************************************************* PP TIGR00839 438 ekdllteeelddilsvenllkpaykakklk 467 e +ll eeelddils++nll+p +k+ ++ NCBI__GCF_001659785.1:WP_067478856.1 458 EMGLLDEEELDDILSPQNLLHPEFKGTRYL 487 ************************999886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (468 nodes) Target sequences: 1 (499 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 20.63 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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