Align argininosuccinate synthase (EC 6.3.4.5) (characterized)
to candidate WP_013430408.1 CALKRO_RS07345 argininosuccinate synthase
Query= BRENDA::A4I066 (418 letters) >NCBI__GCF_000166775.1:WP_013430408.1 Length = 403 Score = 484 bits (1246), Expect = e-141 Identities = 243/402 (60%), Positives = 300/402 (74%), Gaps = 2/402 (0%) Query: 12 KKPRVVLAYSGGLDTSVIIPWLKENYDYEVIACCANVGQGAGEIDGLEEKAKKSGASKLY 71 K +VVLAYSGGLDTSVIIPWLKEN+D EVIA +VGQ + D ++EKA K+GASK+Y Sbjct: 2 KLNKVVLAYSGGLDTSVIIPWLKENFDCEVIAVVVDVGQ-EDDFDAIKEKAYKTGASKVY 60 Query: 72 LLDLREEYVTDYIFPTLKAGATYEGKYMLGTSHARPLIAKHLVEVAHKEGAVAICHGATG 131 + D +EE+V +YIFPTLKAGA YEGKY+LGTS ARPLIAK LV +A KE A AI HGATG Sbjct: 61 IEDAKEEFVNEYIFPTLKAGAIYEGKYLLGTSMARPLIAKKLVNIAKKENADAIAHGATG 120 Query: 132 KGNDQVRFELAVMALDPSLKCVAPWREWNIKSREDAIDYAEAHGVPVPCTKSDLYSRDRN 191 KGNDQVRFE+ + AL P +K +APWR WN+KSRED ++Y G+ +P K + YS D N Sbjct: 121 KGNDQVRFEVTIKALMPQIKIIAPWRIWNLKSREDELNYLTQKGIDIPFKKEESYSMDGN 180 Query: 192 LWHISHEGMDLEDPANEPAYARLLRLCNTVEKAPDEAEYVTVQFEKGIPVAVNGRKMSSV 251 +WH+SHEG+DLEDP N P + ++L++ K D E V ++FEKGIPV VNG++M V Sbjct: 181 IWHLSHEGLDLEDPWNMPDFDKVLKITKNPLKLADLPETVEIEFEKGIPVKVNGQQMGGV 240 Query: 252 ELVEELNALGGKHAIGIEDIVEDRLVGMKSRGVYETPAGTILYKALDMLESLCLDRDTQS 311 EL++ LN +G H IGI DIVE+RLVGMKSRGVYETP GTILY A LE LCLDR T Sbjct: 241 ELLKTLNKIGSNHGIGIADIVENRLVGMKSRGVYETPGGTILYYAHRELEYLCLDRATLH 300 Query: 312 FKRQSAVRFSELVYDGKWFTPLRESMSAMFDQMAETVTGEATLKLYKGNLVPAGAQSPYS 371 FK A+RF+ELVYDG WF+PLRE++SA D+ E V G L LY+GN+ AG++SP S Sbjct: 301 FKDMVAIRFAELVYDGLWFSPLREAISAFVDKTQEVVNGTVRLVLYRGNIYSAGSKSPNS 360 Query: 372 LYNKNIASFGDSQHLYNHHDAEGFIRLFGLPLRVRSMMKAKE 413 LY K++A+F + Q +YN DAEGFI LFGLPL+V M+ KE Sbjct: 361 LYIKDLATFEEDQ-MYNQKDAEGFINLFGLPLKVFGMVNRKE 401 Lambda K H 0.317 0.134 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: 489 Number of extensions: 15 Number of successful extensions: 3 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: 418 Length of database: 403 Length adjustment: 31 Effective length of query: 387 Effective length of database: 372 Effective search space: 143964 Effective search space used: 143964 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: 50 (23.9 bits)
Align candidate WP_013430408.1 CALKRO_RS07345 (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.3133379.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-159 516.3 0.0 3.8e-159 516.1 0.0 1.0 1 NCBI__GCF_000166775.1:WP_013430408.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430408.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 516.1 0.0 3.8e-159 3.8e-159 1 391 [. 5 396 .. 5 399 .. 0.98 Alignments for each domain: == domain 1 score: 516.1 bits; conditional E-value: 3.8e-159 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaa 72 kvvlaysGGlDtsv++++l+e+ +eviav+vdvGq e+d+dai+eka k Ga k y+ Da+eefv++y+f++ NCBI__GCF_000166775.1:WP_013430408.1 5 KVVLAYSGGLDTSVIIPWLKENfDCEVIAVVVDVGQ-EDDFDAIKEKAYKTGASKVYIEDAKEEFVNEYIFPT 76 8*********************99************.8*********************************** PP TIGR00032 73 iqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvrele 145 ++a+a+yegkYll+t++aRpliakklv++akke+a+a+ahG+tgKGnDqvRFe++i++l p++k+iaP+r ++ NCBI__GCF_000166775.1:WP_013430408.1 77 LKAGAIYEGKYLLGTSMARPLIAKKLVNIAKKENADAIAHGATGKGNDQVRFEVTIKALMPQIKIIAPWRIWN 149 ************************************************************************* PP TIGR00032 146 li.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpstepp.ediyelvkdpiektedepevve 216 l Re+e++y+++kGi++p +ke+ ys+D n+++ s+E+ +LEdp+ +p +++ +++k+p + d pe+ve NCBI__GCF_000166775.1:WP_013430408.1 150 LKsREDELNYLTQKGIDIPFKKEESYSMDGNIWHLSHEGLDLEDPWNMPDfDKVLKITKNPLKLA-DLPETVE 221 *88******************************************99986266789999999888.******* PP TIGR00032 217 ieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvl 289 ieFekG+Pv++ng+++ vel++++n+i+ +hG+G DivE+R++g+KsR++YE+p+ ++L Ah++Le l l NCBI__GCF_000166775.1:WP_013430408.1 222 IEFEKGIPVKVNGQQMGGVELLKTLNKIGSNHGIGIADIVENRLVGMKSRGVYETPGGTILYYAHRELEYLCL 294 ************************************************************************* PP TIGR00032 290 tkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelv 362 ++ +l+fk++v +++el+Y Glwf+pl+ea+ a+++ktqe v+Gtvr+ l++Gn +++g ks++slY ++l+ NCBI__GCF_000166775.1:WP_013430408.1 295 DRATLHFKDMVAIRFAELVYDGLWFSPLREAISAFVDKTQEVVNGTVRLVLYRGNIYSAGSKSPNSLYIKDLA 367 ************************************************************************* PP TIGR00032 363 sfekdkefdqkdaiGfikirglqikvyre 391 +fe+d+ ++qkda+Gfi++ gl+ kv+ + NCBI__GCF_000166775.1:WP_013430408.1 368 TFEEDQMYNQKDAEGFINLFGLPLKVFGM 396 ************************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (403 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: 00:00:00.00 # Mc/sec: 16.59 // [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