Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate RR42_RS17170 RR42_RS17170 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >FitnessBrowser__Cup4G11:RR42_RS17170 Length = 409 Score = 490 bits (1261), Expect = e-143 Identities = 242/401 (60%), Positives = 303/401 (75%), Gaps = 6/401 (1%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGASKAIAL-- 59 K+VLAYSGGLDTS+ILKWL++TY+ EV+ FTADIGQGEE+E AR+KAL+ G Sbjct: 6 KVVLAYSGGLDTSVILKWLQDTYQCEVVTFTADIGQGEELEPARQKALKFGIKPENIFID 65 Query: 60 DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119 DL+EEFVRDFVFPM RA AVYEG YLLGTSIARPLIAK + I GA+A++HGATGKG Sbjct: 66 DLREEFVRDFVFPMFRANAVYEGEYLLGTSIARPLIAKRQIEILRSTGADAVSHGATGKG 125 Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQEK---PYSMDA 176 NDQVRFEL Y L+P +KVIAPWREW R++++AYAE GI + + +K PYSMDA Sbjct: 126 NDQVRFELGYYGLEPGVKVIAPWREWDLLSREKLLAYAEKAGIDIDMKHKKGGAPYSMDA 185 Query: 177 NLLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPA 236 NLLHIS+EG LEDP AE + M+R T PE APDA EY++VEF GD V +NG+R++PA Sbjct: 186 NLLHISFEGRHLEDPKAEAEEDMWRWTVSPENAPDAAEYLDVEFEGGDIVGLNGKRMTPA 245 Query: 237 ALLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLH 296 +L LN +GG+HG+GR+D+VENR+VGMKSRG YETPGGTI+ A RA+ES+TLDREV H Sbjct: 246 EVLTELNRLGGKHGIGRLDLVENRYVGMKSRGCYETPGGTIILKAHRAIESITLDREVAH 305 Query: 297 QRDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKS 356 +D L P+YA L+Y G+W++PER ALQ DH V G R+KLYKGNV VV R + + Sbjct: 306 LKDDLMPRYASLIYNGYWWSPERRALQVLIDHTQAKVNGWVRVKLYKGNVIVVARDSKDT 365 Query: 357 LYRQDLVSFDEAGG-YDQKDAEGFIKIQALRLRVRALVERE 396 L+ + + +FD+ GG Y+Q DA GFIK+ ALR+R+ R+ Sbjct: 366 LFDKTIATFDDDGGAYNQADAGGFIKLNALRMRIAENARRQ 406 Lambda K H 0.319 0.137 0.402 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: 542 Number of extensions: 17 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: 400 Length of database: 409 Length adjustment: 31 Effective length of query: 369 Effective length of database: 378 Effective search space: 139482 Effective search space used: 139482 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate RR42_RS17170 RR42_RS17170 (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.30431.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-145 468.8 0.0 1.1e-144 468.5 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS17170 RR42_RS17170 argininosuccinate s Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS17170 RR42_RS17170 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 468.5 0.0 1.1e-144 1.1e-144 1 390 [. 6 401 .. 6 405 .. 0.96 Alignments for each domain: == domain 1 score: 468.5 bits; conditional E-value: 1.1e-144 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGae..kayviDareefvk 66 kvvlaysGGlDtsv+lk+l++ +ev+++t+d+Gq+ e+l+ +++kalk+G + + + D reefv+ lcl|FitnessBrowser__Cup4G11:RR42_RS17170 6 KVVLAYSGGLDTSVILKWLQDTyQCEVVTFTADIGQG-EELEPARQKALKFGIKpeNIFIDDLREEFVR 73 8*********************899***********9.9*************86314555579****** PP TIGR00032 67 dylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdl 135 d++f+ +anavyeg+Yll+t++aRpliak+++e+ + ga+av+hG+tgKGnDqvRFel + l+p + lcl|FitnessBrowser__Cup4G11:RR42_RS17170 74 DFVFPMFRANAVYEGEYLLGTSIARPLIAKRQIEILRSTGADAVSHGATGKGNDQVRFELGYYGLEPGV 142 ********************************************************************* PP TIGR00032 136 kviaPvreleli.ReeeieyaaekGievpvekek...aysiDenllgrsiEageLEdpsteppediyel 200 kviaP+re++l Re++++ya++ Gi++ ++++k +ys+D nll++s E+ +LEdp++e ed++++ lcl|FitnessBrowser__Cup4G11:RR42_RS17170 143 KVIAPWREWDLLsREKLLAYAEKAGIDIDMKHKKggaPYSMDANLLHISFEGRHLEDPKAEAEEDMWRW 211 **********987*****************99876669******************************* PP TIGR00032 201 vkdpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiY 269 +++p++++ d +e++++eFe G v lng++++p e++ ++n+++gkhG+Gr+D vE+R++g+KsR++Y lcl|FitnessBrowser__Cup4G11:RR42_RS17170 212 TVSPENAP-DAAEYLDVEFEGGDIVGLNGKRMTPAEVLTELNRLGGKHGIGRLDLVENRYVGMKSRGCY 279 **998888.************************************************************ PP TIGR00032 270 EapalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrv 338 E+p+ ++++kAh+++e+ +l+++v+++k+ +y+ liY+G+w++p++ al+ li++tq +v+G+vrv lcl|FitnessBrowser__Cup4G11:RR42_RS17170 280 ETPGGTIILKAHRAIESITLDREVAHLKDDLMPRYASLIYNGYWWSPERRALQVLIDHTQAKVNGWVRV 348 ********************************************************************* PP TIGR00032 339 klfkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvyr 390 kl+kGn+iv++r+s+++l+d+++++f+ +++q da Gfik+++l++++ + lcl|FitnessBrowser__Cup4G11:RR42_RS17170 349 KLYKGNVIVVARDSKDTLFDKTIATFDDdGGAYNQADAGGFIKLNALRMRIAE 401 ***************************8446799*************998766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (409 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: 10.24 // [ok]
This GapMind analysis is from Apr 09 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