Align argininosuccinate synthase (characterized)
to candidate WP_011881448.1 argininosuccinate synthase
Query= CharProtDB::CH_024687 (447 letters) >NCBI__GCF_000016205.1:WP_011881448.1 Length = 445 Score = 709 bits (1829), Expect = 0.0 Identities = 349/441 (79%), Positives = 388/441 (87%) Query: 1 MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA 60 M+TIL+ LP GQ++GIAFSGGLDTSAAL WM+ KGAVPYAYTANLGQPDE+DYDAIP+RA Sbjct: 1 MSTILESLPTGQKVGIAFSGGLDTSAALHWMKLKGAVPYAYTANLGQPDEDDYDAIPKRA 60 Query: 61 MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120 +EYGA ARLIDCR QLVAEGIAA+Q GAFH TT G+TYFNTTP+GRAVTGTMLVAAMKE Sbjct: 61 IEYGAAGARLIDCRAQLVAEGIAALQSGAFHITTAGVTYFNTTPIGRAVTGTMLVAAMKE 120 Query: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG 180 DGVNIWGDGSTYKGNDIERFYRYGLL N +L+IYKPWLD FIDELGGR EMSEFM G Sbjct: 121 DGVNIWGDGSTYKGNDIERFYRYGLLVNPDLKIYKPWLDQTFIDELGGRAEMSEFMNQAG 180 Query: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240 F Y+MS EKAYSTDSN+LGATHEAKDLE L S +KIVNPIMGV FW + VKI AEEVTVR Sbjct: 181 FAYRMSAEKAYSTDSNLLGATHEAKDLESLESGIKIVNPIMGVAFWRDDVKIAAEEVTVR 240 Query: 241 FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300 FE G PVALNG F D VE++LEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPG+ALL Sbjct: 241 FEAGQPVALNGVEFKDQVELLLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGLALL 300 Query: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV 360 +IAYERL+TGIHNEDTIEQY +GR+LGRLLYQGRWFD QA+MLR++ QRWVA ITGEV Sbjct: 301 YIAYERLVTGIHNEDTIEQYRENGRRLGRLLYQGRWFDPQAIMLRETAQRWVARAITGEV 360 Query: 361 TLELRRGNDYSILNTVSENLTYKPERLTMEKGDSVFSPDDRIGQLTMRNLDITDTREKLF 420 +ELRRGNDYSIL+T S NLTY+PERL+MEK S FSP DRIGQLTMRNLDITDTR+KL Sbjct: 361 KIELRRGNDYSILSTKSPNLTYQPERLSMEKVASTFSPRDRIGQLTMRNLDITDTRDKLR 420 Query: 421 GYAKTGLLSSSAASGVPQVEN 441 YA+ GLL+ +S +PQ+++ Sbjct: 421 VYAQVGLLTPGESSALPQIKS 441 Lambda K H 0.317 0.135 0.397 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: 663 Number of extensions: 14 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: 447 Length of database: 445 Length adjustment: 32 Effective length of query: 415 Effective length of database: 413 Effective search space: 171395 Effective search space used: 171395 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 WP_011881448.1 (argininosuccinate synthase)
to HMM TIGR00032 (argG: argininosuccinate synthase (EC 6.3.4.5))
# 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/TIGR00032.hmm # target sequence database: /tmp/gapView.24621.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00032 [M=394] Accession: TIGR00032 Description: argG: argininosuccinate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.9e-162 524.8 0.0 1e-161 524.6 0.0 1.0 1 lcl|NCBI__GCF_000016205.1:WP_011881448.1 argininosuccinate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011881448.1 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 524.6 0.0 1e-161 1e-161 1 393 [. 13 419 .. 13 420 .. 0.99 Alignments for each domain: == domain 1 score: 524.6 bits; conditional E-value: 1e-161 TIGR00032 1 kvvlaysGGlDtsvalklleekgaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkdy 68 kv++a+sGGlDts+al++++ kga+++a+t+++Gqp e+d+dai+++a+++Ga a++iD+r+++v++ lcl|NCBI__GCF_000016205.1:WP_011881448.1 13 KVGIAFSGGLDTSAALHWMKLKGAVPYAYTANLGQPdEDDYDAIPKRAIEYGAAGARLIDCRAQLVAE- 80 89******************************************************************. PP TIGR00032 69 lfaaiqanavyegk....YllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnp 133 ++aa+q +a++ ++ Y+++t+++R++++++lv+++k++g++++++G+t+KGnD++RF++++ll np lcl|NCBI__GCF_000016205.1:WP_011881448.1 81 GIAALQSGAFHITTagvtYFNTTPIGRAVTGTMLVAAMKEDGVNIWGDGSTYKGNDIERFYRYGLLVNP 149 *************99999*************************************************** PP TIGR00032 134 dlkviaPvreleli.....ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdp.stepped 196 dlk+++P+++ +i R+e++e++++ G+ ++++ ekays+D+nllg+++Ea++LE + s ++++ lcl|NCBI__GCF_000016205.1:WP_011881448.1 150 DLKIYKPWLDQTFIdelggRAEMSEFMNQAGFAYRMSAEKAYSTDSNLLGATHEAKDLESLeSGIKIVN 218 *************************************************************999***** PP TIGR00032 197 iyelvkdpiektedepevveieFekGvPvalngesle.pvelilkaneiagkhGvGriDivEdRiiglK 264 ++++v+++ +++++ +e+v+++Fe G Pvalng++++ +vel+l+an+i+g+hG+G++D++E+Rii++K lcl|NCBI__GCF_000016205.1:WP_011881448.1 219 PIMGVAFWRDDVKIAAEEVTVRFEAGQPVALNGVEFKdQVELLLEANRIGGRHGLGMSDQIENRIIEAK 287 ************************************99******************************* PP TIGR00032 265 sReiYEapalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaeal.dalikktqerv 332 sR+iYEap+l+lL +A+++L+t+++++d++e+++ +++++++l+Y+G+wfdp+a +l +++++++++++ lcl|NCBI__GCF_000016205.1:WP_011881448.1 288 SRGIYEAPGLALLYIAYERLVTGIHNEDTIEQYRENGRRLGRLLYQGRWFDPQAIMLrETAQRWVARAI 356 *********************************************************99********** PP TIGR00032 333 tGtvrvklfkGnaivigrk.seyslYdeelvsfek.dkefdqkdaiGfikirglqikvyrekl 393 tG+v+++l++Gn+++i+ + s++++Y++e++s+ek ++f+++d+iG++++r+l+i+++r kl lcl|NCBI__GCF_000016205.1:WP_011881448.1 357 TGEVKIELRRGNDYSILSTkSPNLTYQPERLSMEKvASTFSPRDRIGQLTMRNLDITDTRDKL 419 ****************9998***************999*********************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (445 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: 11.64 // [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