Align argininosuccinate synthase (EC 6.3.4.5) (characterized)
to candidate WP_012282529.1 HM1_RS06565 argininosuccinate synthase
Query= BRENDA::A4I066 (418 letters) >NCBI__GCF_000019165.1:WP_012282529.1 Length = 403 Score = 519 bits (1336), Expect = e-152 Identities = 257/398 (64%), Positives = 311/398 (78%), Gaps = 3/398 (0%) Query: 15 RVVLAYSGGLDTSVIIPWLKENYDYEVIACCANVGQGAGEIDGLEEKAKKSGASKLYLLD 74 ++VLAYSGGLDTS+IIPWLKENY YEVIA A++GQG E+ L EKA KSGA+KLY+ D Sbjct: 4 KIVLAYSGGLDTSIIIPWLKENYGYEVIAMAADLGQGE-ELAPLNEKAIKSGATKLYIED 62 Query: 75 LREEYVTDYIFPTLKAGATYEGKYMLGTSHARPLIAKHLVEVAHKEGAVAICHGATGKGN 134 ++EE+VTD+I+PTLKAGA YEGKY+LGTS ARPLIAK LVE+A EGA AI HGATGKGN Sbjct: 63 VKEEFVTDFIWPTLKAGAVYEGKYLLGTSFARPLIAKRLVEIARAEGAEAIAHGATGKGN 122 Query: 135 DQVRFELAVMALDPSLKCVAPWREWNIKSREDAIDYAEAHGVPVPCTKSDLYSRDRNLWH 194 DQVRFEL V AL P LK VAPWREW+I+SREDAIDYA A +PVP K YS DRNLWH Sbjct: 123 DQVRFELTVKALAPDLKIVAPWREWDIRSREDAIDYANARNIPVPVKKDRPYSMDRNLWH 182 Query: 195 ISHEGMDLEDPANEPAYARLLRLCNTVEKAPDEAEYVTVQFEKGIPVAVNGRKMSSVELV 254 +SHEG DLEDP NEP L +C E+APD+ EYV + F KGIPV +NG + VE++ Sbjct: 183 LSHEGADLEDPWNEP-QNDLFMICTAPEQAPDKPEYVEIDFAKGIPVKLNGEALGPVEMI 241 Query: 255 EELNALGGKHAIGIEDIVEDRLVGMKSRGVYETPAGTILYKALDMLESLCLDRDTQSFKR 314 E+LNA+ H +GI D+VE+RLVGMKSRGVYETPAGT+LY A LE LCLDR T +K Sbjct: 242 EKLNAIAAAHGVGICDMVENRLVGMKSRGVYETPAGTVLYAAHRELEYLCLDRATMHYKE 301 Query: 315 QSAVRFSELVYDGKWFTPLRESMSAMFDQMAETVTGEATLKLYKGNLVPAGAQSPYSLYN 374 Q A+R++ELVYDG W+ PLRE++ A + ETVTG +KLYKG++ PAGA+SPYSLYN Sbjct: 302 QVALRYAELVYDGVWYHPLREALDAFVNVTQETVTGTVRMKLYKGSVTPAGAKSPYSLYN 361 Query: 375 KNIASFGDSQHLYNHHDAEGFIRLFGLPLRVRSMMKAK 412 + ++FG + +YN DAEGFI LFGLPL+VR++M+ K Sbjct: 362 EEFSTFGRDE-VYNQKDAEGFINLFGLPLKVRAIMEQK 398 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: 531 Number of extensions: 20 Number of successful extensions: 4 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_012282529.1 HM1_RS06565 (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.26579.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-160 518.3 0.0 1e-159 518.0 0.0 1.0 1 lcl|NCBI__GCF_000019165.1:WP_012282529.1 HM1_RS06565 argininosuccinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000019165.1:WP_012282529.1 HM1_RS06565 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 518.0 0.0 1e-159 1e-159 1 389 [. 4 392 .. 4 397 .. 0.98 Alignments for each domain: == domain 1 score: 518.0 bits; conditional E-value: 1e-159 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdy 68 k+vlaysGGlDts+++++l+e+ g+evia+++d+Gq+ e+l+ +eka+k Ga+k y+ D +eefv+d+ lcl|NCBI__GCF_000019165.1:WP_012282529.1 4 KIVLAYSGGLDTSIIIPWLKENyGYEVIAMAADLGQG-EELAPLNEKAIKSGATKLYIEDVKEEFVTDF 71 89**********************************9.9****************************** PP TIGR00032 69 lfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkv 137 + ++++a+avyegkYll+t+ aRpliak+lve+a+ egaea+ahG+tgKGnDqvRFel++++l+pdlk+ lcl|NCBI__GCF_000019165.1:WP_012282529.1 72 IWPTLKAGAVYEGKYLLGTSFARPLIAKRLVEIARAEGAEAIAHGATGKGNDQVRFELTVKALAPDLKI 140 ********************************************************************* PP TIGR00032 138 iaPvreleli.ReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpi 205 +aP+re+++ Re+ i+ya+++ i+vpv+k+++ys+D+nl++ s+E+ +LEdp+ ep +d +++ p+ lcl|NCBI__GCF_000019165.1:WP_012282529.1 141 VAPWREWDIRsREDAIDYANARNIPVPVKKDRPYSMDRNLWHLSHEGADLEDPWNEPQNDLFMICTAPE 209 ********988*****************************************************99777 PP TIGR00032 206 ektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapal 274 +++ d+pe+vei+F kG+Pv+lnge l pve+i+k+n ia +hGvG D+vE+R++g+KsR++YE+pa lcl|NCBI__GCF_000019165.1:WP_012282529.1 210 QAP-DKPEYVEIDFAKGIPVKLNGEALGPVEMIEKLNAIAAAHGVGICDMVENRLVGMKSRGVYETPAG 277 777.***************************************************************** PP TIGR00032 275 llLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkG 343 ++L Ah++Le l l++ ++++ke v +y+el+Y G+w++pl+ealda+++ tqe vtGtvr+kl+kG lcl|NCBI__GCF_000019165.1:WP_012282529.1 278 TVLYAAHRELEYLCLDRATMHYKEQVALRYAELVYDGVWYHPLREALDAFVNVTQETVTGTVRMKLYKG 346 ********************************************************************* PP TIGR00032 344 naivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqikvy 389 +++ +g ks+yslY+ee ++f +d+ ++qkda+Gfi++ gl+ kv lcl|NCBI__GCF_000019165.1:WP_012282529.1 347 SVTPAGAKSPYSLYNEEFSTFGRDEVYNQKDAEGFINLFGLPLKVR 392 *****************************************98875 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.73 // [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