Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate Pf6N2E2_4085 Aspartate ammonia-lyase (EC 4.3.1.1)
Query= BRENDA::Q9HTD7 (474 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 Length = 478 Score = 826 bits (2133), Expect = 0.0 Identities = 426/474 (89%), Positives = 442/474 (93%) Query: 1 MSPVASSRIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAA 60 MS AS R EKDLLG LEVPA AYYGIQTLRAVNNFRLSGVP+SHYPKLVV LAMVKQAA Sbjct: 5 MSSAASFRTEKDLLGVLEVPAQAYYGIQTLRAVNNFRLSGVPISHYPKLVVGLAMVKQAA 64 Query: 61 ADANRQLGHLPEDKHAAISEACARLIRGDFHEQFVVDMIQGGAGTSTNMNANEVIANIAL 120 ADANR+LG L E KHAAISEACARLIRGDFHE+FVVDMIQGGAGTSTNMNANEVIANIAL Sbjct: 65 ADANRELGQLSEAKHAAISEACARLIRGDFHEEFVVDMIQGGAGTSTNMNANEVIANIAL 124 Query: 121 EAMGHTKGEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDTLLASLDSLIQAFAAKGV 180 EAMGH KGEY+YLHPNNDVNMAQSTNDAYPTAIRLGLLLGHD LLASLDSLIQAFAAKG Sbjct: 125 EAMGHQKGEYQYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDALLASLDSLIQAFAAKGE 184 Query: 181 EFAGVLKMGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLTEVNLGGTAIGTG 240 EF+ VLKMGRTQLQDAVPMTLGQEF AFATTL EDL RL+ LAPELLTEVNLGGTAIGTG Sbjct: 185 EFSHVLKMGRTQLQDAVPMTLGQEFRAFATTLSEDLARLKTLAPELLTEVNLGGTAIGTG 244 Query: 241 INADPGYQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300 INADP YQ LAV+RLA ISGQPL PAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL Sbjct: 245 INADPRYQALAVQRLATISGQPLVPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 304 Query: 301 RLLSSGPRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQ 360 RLLSSGPRTGINEINLP RQPGSSIMPGKVNPVIPEAVNQVAF++IGNDLALT+AAEGGQ Sbjct: 305 RLLSSGPRTGINEINLPARQPGSSIMPGKVNPVIPEAVNQVAFQIIGNDLALTIAAEGGQ 364 Query: 361 LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPY 420 LQLNVMEPLIA+KIFDSIRLLQRAMDMLREHCI GITAN RC ELVEHSIGLVTALNPY Sbjct: 365 LQLNVMEPLIAFKIFDSIRLLQRAMDMLREHCIVGITANEARCRELVEHSIGLVTALNPY 424 Query: 421 IGYENSTRIAKTALESGRGVLELVREEKLLDEATLADILLPENMIAPRLIPLRA 474 IGYEN+TRIA+ ALESGRGVLELVREE LLD+A L DIL PENMIAPRL+PL+A Sbjct: 425 IGYENATRIARVALESGRGVLELVREEGLLDDAMLDDILRPENMIAPRLVPLKA 478 Lambda K H 0.318 0.135 0.380 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: 806 Number of extensions: 19 Number of successful extensions: 2 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: 474 Length of database: 478 Length adjustment: 33 Effective length of query: 441 Effective length of database: 445 Effective search space: 196245 Effective search space used: 196245 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: 51 (24.3 bits)
Align candidate Pf6N2E2_4085 (Aspartate ammonia-lyase (EC 4.3.1.1))
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.689.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-211 686.8 0.0 9.9e-211 686.5 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 Aspartate ammonia-lyase (EC 4.3. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 Aspartate ammonia-lyase (EC 4.3.1.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 686.5 0.0 9.9e-211 9.9e-211 1 460 [. 12 472 .. 12 477 .. 0.99 Alignments for each domain: == domain 1 score: 686.5 bits; conditional E-value: 9.9e-211 TIGR00839 1 riekdllGekeveaevyyGiqtlrasenfaisnekisdvpefvkalvlvkkaaalanvelkaid 64 r ekdllG ev+a++yyGiqtlra++nf +s++ is++p++v +l++vk+aaa an el++++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 12 RTEKDLLGVLEVPAQAYYGIQTLRAVNNFRLSGVPISHYPKLVVGLAMVKQAAADANRELGQLS 75 89************************************************************** PP TIGR00839 65 ekiakaivaacdeileGkyldqfivdviqGGaGtsvnmntnevianlalellGhkkGeyqflnp 128 e ai +ac ++ G ++++f+vd+iqGGaGts+nmn+nevian+ale +Gh+kGeyq+l+p lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 76 EAKHAAISEACARLIRGDFHEEFVVDMIQGGAGTSTNMNANEVIANIALEAMGHQKGEYQYLHP 139 **************************************************************** PP TIGR00839 129 ndhvnksqstndayptalkiavyesleklvdkiealrdafeqkakefadvlkmGrtqlqdavpl 192 n+ vn++qstndaypta+++ ++ l++++++l +af+ k +ef +vlkmGrtqlqdavp+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 140 NNDVNMAQSTNDAYPTAIRLGLLLGHDALLASLDSLIQAFAAKGEEFSHVLKMGRTQLQDAVPM 203 **************************************************************** PP TIGR00839 193 tlGqefeayalllerdvkrikr.trelllevnlGataiGtGlnadkeysklvvkklaevtGlpl 255 tlGqef+a+a l +d+ r+k + ell evnlG+taiGtG+nad+ y+ l+v++la ++G pl lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 204 TLGQEFRAFATTLSEDLARLKTlAPELLTEVNLGGTAIGTGINADPRYQALAVQRLATISGQPL 267 ********************98355899************************************ PP TIGR00839 256 vpaenlieatsdtgayvevsgalkriavklskvcndlrllssGpraGlneinlpelqaGssimp 319 vpa +lieatsd ga+v sg lkr+avklsk+cndlrllssGpr+G+neinlp++q+Gssimp lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 268 VPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDLRLLSSGPRTGINEINLPARQPGSSIMP 331 **************************************************************** PP TIGR00839 320 akvnpvvpevvnqvcfkviGndttvtlaaeaGqlqlnvlepviafallesisiltnaiesltdk 383 +kvnpv+pe vnqv+f++iGnd ++t+aae+Gqlqlnv+ep+iaf++++si +l++a+ l+++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 332 GKVNPVIPEAVNQVAFQIIGNDLALTIAAEGGQLQLNVMEPLIAFKIFDSIRLLQRAMDMLREH 395 **************************************************************** PP TIGR00839 384 cveGitanekicedyvfnsiGivtalnpfiGyekaalvakeaiktgksvrdvvlekdllteeel 447 c+ Gitane +c++ v++siG+vtalnp+iGye+a ++a++a+++g++v ++v e++ll ++ l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 396 CIVGITANEARCRELVEHSIGLVTALNPYIGYENATRIARVALESGRGVLELVREEGLLDDAML 459 **************************************************************** PP TIGR00839 448 ddilsvenllkpa 460 ddil++en++ p lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4085 460 DDILRPENMIAPR 472 **********995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (468 nodes) Target sequences: 1 (478 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: 00:00:00.02 # Mc/sec: 10.79 // [ok]
This GapMind analysis is from Sep 17 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