Align arginosuccinate synthetase (EC 6.3.4.5) (characterized)
to candidate Echvi_3846 Echvi_3846 argininosuccinate synthase
Query= reanno::Btheta:353286 (402 letters) >FitnessBrowser__Cola:Echvi_3846 Length = 399 Score = 464 bits (1195), Expect = e-135 Identities = 222/389 (57%), Positives = 286/389 (73%) Query: 6 KKVVVAFSGGLDTSFTVMYLAKEKGYEVYAACANTGGFSEEQLKTNEENAYKLGAVKYVT 65 KKVV+A+SGGLDT+F ++L++EKGYEV+A NTGGFSEE+LKT EE A KLG + Sbjct: 2 KKVVLAYSGGLDTTFCAIHLSQEKGYEVHAVLVNTGGFSEEELKTTEERAGKLGIASFKV 61 Query: 66 LDVTQEYYEKSLKYMVFGNVLRNGTYPISVSSERIFQALAIARYANEIGADAIAHGSTGA 125 LDVTQ YY + +KY++FGNVL+N TYP+SVS+ERI QA A+A YA +IGA A+AHGSTGA Sbjct: 62 LDVTQTYYNEVIKYLIFGNVLKNQTYPLSVSAERILQAKALAEYAKQIGAKAVAHGSTGA 121 Query: 126 GNDQIRFDMTFLVLAPNVEIITLTRDMALSRQEEIDYLNKHGFSADFTKLKYSYNVGLWG 185 GNDQ+RFDM F + P EIIT RD+ LSR+ EI++L KHG +F K KYS N G+WG Sbjct: 122 GNDQVRFDMIFQTILPEAEIITPIRDLQLSREAEIEFLKKHGVEMNFEKAKYSINKGIWG 181 Query: 186 TSICGGEILDSAQGLPETAYLKHVEKEGSEQLRLTFEKGELKAVNDETFDDPIQAIQKVE 245 TS+ G E L S LPE AY + KE Q+ L FE GEL VN + F +P+ AI KV+ Sbjct: 182 TSVGGKETLTSGDTLPEEAYPTQLTKETPTQISLQFEAGELVGVNGQKFSNPVDAILKVQ 241 Query: 246 EIGAAYGIGRDMHVGDTIIGIKGRVGFEAAAPMLIIGAHRFLEKYTLSKWQQYWKDQVAN 305 + Y IGRD+HVGDTIIGIKGRVGFEAAAP++II AH+ LEK+TL+KWQ +WK+Q++ Sbjct: 242 ALADPYAIGRDIHVGDTIIGIKGRVGFEAAAPLIIIKAHQLLEKHTLTKWQTFWKNQLSE 301 Query: 306 WYGMFLHESQYLEPVMRDIEAMLQESQRNVNGTAILELRPLSFSTVGVESEDDLVKTKFG 365 +YG LHE YL+PVMR++EA L ++Q+ V+G + L+P F +G++S DL+ KFG Sbjct: 302 FYGNHLHEGHYLDPVMRNLEAFLADTQQFVSGEVKVALKPYQFQLIGIDSPHDLMSAKFG 361 Query: 366 EYGEMQKGWTAEDAKGFIKVTSTPLRVYY 394 YGEM KG+TAED KGF K+ +Y+ Sbjct: 362 SYGEMNKGYTAEDVKGFTKILGNQTAIYH 390 Lambda K H 0.316 0.134 0.385 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: 490 Number of extensions: 19 Number of successful extensions: 1 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: 402 Length of database: 399 Length adjustment: 31 Effective length of query: 371 Effective length of database: 368 Effective search space: 136528 Effective search space used: 136528 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 Echvi_3846 Echvi_3846 (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.1665.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-85 272.1 0.2 5.8e-85 271.9 0.2 1.0 1 lcl|FitnessBrowser__Cola:Echvi_3846 Echvi_3846 argininosuccinate syn Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_3846 Echvi_3846 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 271.9 0.2 5.8e-85 5.8e-85 1 392 [. 3 392 .. 3 394 .. 0.95 Alignments for each domain: == domain 1 score: 271.9 bits; conditional E-value: 5.8e-85 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqp.eedldaieekalklGaekayviDareefvkdylfaa 72 kvvlaysGGlDt+ + +l ++ g+ev av v+ G ee+l++ ee+a klG + v+D + + ++++ lcl|FitnessBrowser__Cola:Echvi_3846 3 KVVLAYSGGLDTTFCAIHLSQEkGYEVHAVLVNTGGFsEEELKTTEERAGKLGIASFKVLDVTQTYYNEVIKYL 76 8************8876666555***********9877*******************************99999 PP TIGR00032 73 iqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvrelel 146 i n + +++Y+ls + R l ak+l e ak+ ga+avahG+tg GnDqvRF++++++ p+ ++i+P+r+l+l lcl|FitnessBrowser__Cola:Echvi_3846 77 IFGNVLKNQTYPLSVSAERILQAKALAEYAKQIGAKAVAHGSTGAGNDQVRFDMIFQTILPEAEIITPIRDLQL 150 ************************************************************************** PP TIGR00032 147 iReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFe 220 +Re eie+++++G+e++ ek +ysi++ ++g s+ ++e + pe++y + t+++p ++ ++Fe lcl|FitnessBrowser__Cola:Echvi_3846 151 SREAEIEFLKKHGVEMNFEK-AKYSINKGIWGTSVGGKETLTSGDTLPEEAYPTQ-----LTKETPTQISLQFE 218 *******************7.78**************987777667778888544.....467889******** PP TIGR00032 221 kGvPvalngesle.pvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdv 293 G v +ng++++ pv+ ilk++ +a +Gr +v d iig+K R +Ea+a l++ikAh+ Le+ +ltk + lcl|FitnessBrowser__Cola:Echvi_3846 219 AGELVGVNGQKFSnPVDAILKVQALADPYAIGRDIHVGDTIIGIKGRVGFEAAAPLIIIKAHQLLEKHTLTKWQ 292 ************************************************************************** PP TIGR00032 294 lefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfek. 366 + +k+ +e y++ + +G ++dp + +l+a++ tq+ v+G+v+v l + ig +s++ l +++ s+ + lcl|FitnessBrowser__Cola:Echvi_3846 293 TFWKNQLSEFYGNHLHEGHYLDPVMRNLEAFLADTQQFVSGEVKVALKPYQFQLIGIDSPHDLMSAKFGSYGEm 366 ***********************************************************************987 PP TIGR00032 367 dkefdqkdaiGfikirglqikvyrek 392 +k + +d +Gf ki g q+++y+++ lcl|FitnessBrowser__Cola:Echvi_3846 367 NKGYTAEDVKGFTKILGNQTAIYHKV 392 99***************999999875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (399 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: 9.31 // [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