Align Argininosuccinate synthase; Citrulline--aspartate ligase; EC 6.3.4.5 (characterized)
to candidate CCNA_00128 CCNA_00128 argininosuccinate synthase
Query= SwissProt::P59846 (400 letters) >FitnessBrowser__Caulo:CCNA_00128 Length = 408 Score = 487 bits (1253), Expect = e-142 Identities = 248/401 (61%), Positives = 302/401 (75%), Gaps = 5/401 (1%) Query: 2 KIVLAYSGGLDTSIILKWLKETYRAEVIAFTADIGQGEEVEEAREKALRTGAS--KAIAL 59 K+VLAYSGGLDTSIILKWL+ Y AEVI FTAD+GQGEE+E AR KAL G Sbjct: 8 KVVLAYSGGLDTSIILKWLQTEYGAEVITFTADLGQGEEIEPARAKALAAGVKPENIFIE 67 Query: 60 DLKEEFVRDFVFPMMRAGAVYEGYYLLGTSIARPLIAKHLVRIAEEEGAEAIAHGATGKG 119 D++EEFVRD+VFPM RA VYEG YLLGTSIARPLIAK + IA + GA+A++HGATGKG Sbjct: 68 DVREEFVRDYVFPMFRANTVYEGQYLLGTSIARPLIAKKQIEIARKMGADAVSHGATGKG 127 Query: 120 NDQVRFELTAYALKPDIKVIAPWREWSFQGRKEMIAYAEAHGIPVPVTQ--EKPYSMDAN 177 NDQVRFEL Y L+PDI VIAPWREW F+ R+ ++ +AE H I + + E P+S+DAN Sbjct: 128 NDQVRFELGYYGLEPDITVIAPWREWDFKSREALLDFAEKHQIQITKDKRGEAPFSVDAN 187 Query: 178 LLHISYEGGVLEDPWAEPPKGMFRMTQDPEEAPDAPEYVEVEFFEGDPVAVNGERLSPAA 237 LLH S EG VLEDP E P+ + T PE+APDAP + ++F +GDPVA++G +SPA Sbjct: 188 LLHSSSEGKVLEDPAVEAPEFVHMRTIAPEDAPDAPTIITIDFEKGDPVAIDGVAMSPAT 247 Query: 238 LLQRLNEIGGRHGVGRVDIVENRFVGMKSRGVYETPGGTILYHARRAVESLTLDREVLHQ 297 LL +LNE+G +GVGR+D+VENRFVGMKSRGVYETPGGTIL A R +ES+TLDR +H Sbjct: 248 LLTKLNELGRDNGVGRLDLVENRFVGMKSRGVYETPGGTILLAAHRGIESITLDRGAMHL 307 Query: 298 RDMLSPKYAELVYYGFWYAPEREALQAYFDHVARSVTGVARLKLYKGNVYVVGRKAPKSL 357 +D L PKYA LVY GFW++PERE LQA D+ VTG R+KLYKGNV V+GR++P SL Sbjct: 308 KDELMPKYASLVYNGFWFSPEREMLQAAIDYSQDKVTGRVRVKLYKGNVTVIGRESPYSL 367 Query: 358 YRQDLVSFDEAG-GYDQKDAEGFIKIQALRLRVRALVEREG 397 Y QDLV+F+E YD +DA GFIK+ ALRLRV A ++ G Sbjct: 368 YDQDLVTFEEGKVAYDHRDAGGFIKLNALRLRVLAKRDKRG 408 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: 516 Number of extensions: 18 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: 408 Length adjustment: 31 Effective length of query: 369 Effective length of database: 377 Effective search space: 139113 Effective search space used: 139113 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 CCNA_00128 CCNA_00128 (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.324.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-146 473.6 0.0 3.6e-146 473.4 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_00128 CCNA_00128 argininosuccinate syn Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_00128 CCNA_00128 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 473.4 0.0 3.6e-146 3.6e-146 1 391 [. 8 403 .. 8 406 .. 0.97 Alignments for each domain: == domain 1 score: 473.4 bits; conditional E-value: 3.6e-146 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqpeedldaieekalklGae..kayviDareefvkdylf 70 kvvlaysGGlDts++lk+l+ + gaevi++t+d+Gq+ e+++ ++ kal+ G++ + + D reefv+dy+f lcl|FitnessBrowser__Caulo:CCNA_00128 8 KVVLAYSGGLDTSIILKWLQTEyGAEVITFTADLGQG-EEIEPARAKALAAGVKpeNIFIEDVREEFVRDYVF 79 8*********************9*************9.9*************863266677************ PP TIGR00032 71 aaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvre 143 + +an+vyeg+Yll+t++aRpliakk++e+a+k ga+av+hG+tgKGnDqvRFel + l+pd+ viaP+re lcl|FitnessBrowser__Caulo:CCNA_00128 80 PMFRANTVYEGQYLLGTSIARPLIAKKQIEIARKMGADAVSHGATGKGNDQVRFELGYYGLEPDITVIAPWRE 152 ************************************************************************* PP TIGR00032 144 leli.ReeeieyaaekGievpvek..ekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepe 213 +++ Re ++++a+++ i++ +k e ++s+D nll+ s E++ LEdp +e pe +++ + p++++ d p lcl|FitnessBrowser__Caulo:CCNA_00128 153 WDFKsREALLDFAEKHQIQITKDKrgEAPFSVDANLLHSSSEGKVLEDPAVEAPEFVHMRTIAPEDAP-DAPT 224 ***88**************998875579*********************************9787777.**** PP TIGR00032 214 vveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLet 286 +++i+FekG Pva++g+ ++p +l+ k+ne+++ +GvGr+D vE+R +g+KsR++YE+p+ ++L+ Ah+ +e+ lcl|FitnessBrowser__Caulo:CCNA_00128 225 IITIDFEKGDPVAIDGVAMSPATLLTKLNELGRDNGVGRLDLVENRFVGMKSRGVYETPGGTILLAAHRGIES 297 ************************************************************************* PP TIGR00032 287 lvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYde 359 +l++ +++k+ ky+ l+Y+G+wf+p++e+l+a+i+ +q++vtG vrvkl+kGn++vigr+s+yslYd+ lcl|FitnessBrowser__Caulo:CCNA_00128 298 ITLDRGAMHLKDELMPKYASLVYNGFWFSPEREMLQAAIDYSQDKVTGRVRVKLYKGNVTVIGRESPYSLYDQ 370 ************************************************************************* PP TIGR00032 360 elvsfek.dkefdqkdaiGfikirglqikvyre 391 +lv+fe+ + ++d++da Gfik+++l+ +v ++ lcl|FitnessBrowser__Caulo:CCNA_00128 371 DLVTFEEgKVAYDHRDAGGFIKLNALRLRVLAK 403 ******98889***************9988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (408 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: 00:00:00.02 # Mc/sec: 7.73 // [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