Align argininosuccinate synthase (characterized)
to candidate WP_037574015.1 BS73_RS18735 argininosuccinate synthase
Query= CharProtDB::CH_024687 (447 letters) >NCBI__GCF_000744815.1:WP_037574015.1 Length = 485 Score = 597 bits (1539), Expect = e-175 Identities = 289/434 (66%), Positives = 345/434 (79%), Gaps = 1/434 (0%) Query: 1 MTTILKHLPVGQRIGIAFSGGLDTSAALLWMRQKGAVPYAYTANLGQPDEEDYDAIPRRA 60 M+ +L LPVG+R+GIAFSGGLDTS A+ WMR+KGAVP +TA+LGQ DE D ++P RA Sbjct: 1 MSKVLSSLPVGERVGIAFSGGLDTSVAVAWMREKGAVPCTFTADLGQYDEPDIASVPGRA 60 Query: 61 MEYGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKE 120 YGAE +RL+DCR LV EG+AA+ CGAFH +GG YFNTTPLGRAVTGTMLV AM E Sbjct: 61 GAYGAELSRLVDCRAALVEEGLAALTCGAFHIRSGGRPYFNTTPLGRAVTGTMLVRAMLE 120 Query: 121 DGVNIWGDGSTYKGNDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACG 180 D V IWGDGSTYKGNDIERFYRYGLL N L+IYKPWLD +F+ ELGGR EMSE+++A Sbjct: 121 DDVQIWGDGSTYKGNDIERFYRYGLLANPALRIYKPWLDAEFVGELGGRTEMSEWLLARD 180 Query: 181 FDYKMSVEKAYSTDSNMLGATHEAKDLEYLNSSVKIVNPIMGVKFWDESVKIPAEEVTVR 240 Y+ S EKAYSTD+N+ GATHEAK LE+L++ V++V PIMGV+FWD V+I AE+VT+ Sbjct: 181 LPYRASTEKAYSTDANIWGATHEAKALEHLDNGVELVEPIMGVRFWDPEVEIAAEDVTIA 240 Query: 241 FEQGHPVALNGKTFSDDVEMMLEANRIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300 F+QG PVA+NGK F V+++LEAN IGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL Sbjct: 241 FQQGRPVAINGKEFPSAVDLVLEANAIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALL 300 Query: 301 HIAYERLLTGIHNEDTIEQYHAHGRQLGRLLYQGRWFDSQALMLRDSLQRWVASQITGEV 360 AYERL+ IHNEDT+ YH GR+LGRLLY+GRW D QALM+R+SLQRWV S +TGEV Sbjct: 301 FAAYERLVNAIHNEDTVAAYHNEGRRLGRLLYEGRWLDPQALMIRESLQRWVGSAVTGEV 360 Query: 361 TLELRRGNDYSILNTVSENLTYKPERLTMEK-GDSVFSPDDRIGQLTMRNLDITDTREKL 419 TL LRRG DYS++NT +Y P++L+ME+ DS F P DRIGQLTMRNLDI D+R +L Sbjct: 361 TLRLRRGEDYSVINTTGPAFSYHPDKLSMERTEDSAFGPTDRIGQLTMRNLDIADSRSRL 420 Query: 420 FGYAKTGLLSSSAA 433 Y GL+ + Sbjct: 421 EQYTALGLIGGEGS 434 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: 677 Number of extensions: 22 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: 447 Length of database: 485 Length adjustment: 33 Effective length of query: 414 Effective length of database: 452 Effective search space: 187128 Effective search space used: 187128 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_037574015.1 BS73_RS18735 (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.970637.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-142 459.6 0.0 6.5e-142 459.4 0.0 1.0 1 NCBI__GCF_000744815.1:WP_037574015.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000744815.1:WP_037574015.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.4 0.0 6.5e-142 6.5e-142 1 392 [. 13 419 .. 13 421 .. 0.98 Alignments for each domain: == domain 1 score: 459.4 bits; conditional E-value: 6.5e-142 TIGR00032 1 kvvlaysGGlDtsvalklleekgaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkdylfaa 72 +v++a+sGGlDtsva+++++ekga++ ++t+d+Gq e d+++++ +a ++Gae ++++D+r+ +v++ ++aa NCBI__GCF_000744815.1:WP_037574015.1 13 RVGIAFSGGLDTSVAVAWMREKGAVPCTFTADLGQYdEPDIASVPGRAGAYGAELSRLVDCRAALVEE-GLAA 84 69*********************************9899*****************************.**** PP TIGR00032 73 iqanavyegk....YllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPv 141 + ++a++ Y+++t+L+R++++++lv ++ +++++++++G+t+KGnD++RF++++ll np l++++P+ NCBI__GCF_000744815.1:WP_037574015.1 85 LTCGAFHIRSggrpYFNTTPLGRAVTGTMLVRAMLEDDVQIWGDGSTYKGNDIERFYRYGLLANPALRIYKPW 157 ********99999************************************************************ PP TIGR00032 142 releli.....ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdp.steppediyelvkdpiekt 208 ++ e++ R+e++e++ ++ +++++++ekays+D n++g+++Ea+ LE++ + + ++++++v++++ ++ NCBI__GCF_000744815.1:WP_037574015.1 158 LDAEFVgelggRTEMSEWLLARDLPYRASTEKAYSTDANIWGATHEAKALEHLdNGVELVEPIMGVRFWDPEV 230 *****************************************************889***************** PP TIGR00032 209 edepevveieFekGvPvalngesle.pvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikA 280 e+ +e+v+i+F++G Pva+ng+++ +v+l+l+an i+g+hG+G++D++E+Rii++KsR+iYEap+++lL A NCBI__GCF_000744815.1:WP_037574015.1 231 EIAAEDVTIAFQQGRPVAINGKEFPsAVDLVLEANAIGGRHGLGMSDQIENRIIEAKSRGIYEAPGMALLFAA 303 ************************99*********************************************** PP TIGR00032 281 hkdLetlvltkdvlefkeiveekyseliYkGlwfdplaeal.dalikktqervtGtvrvklfkGnaivigrk. 351 +++L++ ++++d++ ++ ++++++l+Y+G+w+dp+a ++ ++l++++ ++vtG+v+++l++G+++++ ++ NCBI__GCF_000744815.1:WP_037574015.1 304 YERLVNAIHNEDTVAAYHNEGRRLGRLLYEGRWLDPQALMIrESLQRWVGSAVTGEVTLRLRRGEDYSVINTt 376 *****************************************99************************999998 PP TIGR00032 352 seyslYdeelvsfek..dkefdqkdaiGfikirglqikvyrek 392 + Y+++++s+e+ d++f ++d+iG++++r+l+i++ r++ NCBI__GCF_000744815.1:WP_037574015.1 377 GPAFSYHPDKLSMERteDSAFGPTDRIGQLTMRNLDIADSRSR 419 99************988999*****************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (485 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 30.93 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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