Align arginosuccinate synthetase (EC 6.3.4.5) (characterized)
to candidate CA265_RS18545 CA265_RS18545 argininosuccinate synthase
Query= reanno::Btheta:353286 (402 letters) >FitnessBrowser__Pedo557:CA265_RS18545 Length = 395 Score = 442 bits (1137), Expect = e-129 Identities = 214/389 (55%), Positives = 285/389 (73%), Gaps = 1/389 (0%) Query: 6 KKVVVAFSGGLDTSFTVMYLAKEKGYEVYAACANTGGFSEEQLKTNEENAYKLGAVKYVT 65 KKVV+AFSGGLDTSF +YLA+++G EV++ NTGGFS+E+L+ E+ AY LG + Sbjct: 2 KKVVLAFSGGLDTSFCCIYLAQDRGLEVHSVIVNTGGFSDEELQEIEKRAYALGVKSHAV 61 Query: 66 LDVTQEYYEKSLKYMVFGNVLRNGTYPISVSSERIFQALAIARYANEIGADAIAHGSTGA 125 +D T+ YYE +KY+VFGNVL+N TYP+SVS+ER+ QA AIA Y +IGAD +AHGSTGA Sbjct: 62 VDETESYYEGCIKYLVFGNVLKNATYPLSVSAERVSQATAIANYVKKIGADYVAHGSTGA 121 Query: 126 GNDQIRFDMTFLVLAPNVEIITLTRDMALSRQEEIDYLNKHGFSADFTKLKYSYNVGLWG 185 GNDQ+RFDM F +L P VEIIT RD+ LSR+ EI+YL +HG K +YS N GLWG Sbjct: 122 GNDQVRFDMIFNILIPEVEIITPIRDLKLSREAEIEYLAQHGVEYSAEKARYSINKGLWG 181 Query: 186 TSICGGEILDSAQGLPETAYLKHVEKEGSEQLRLTFEKGELKAVNDETFDDPIQAIQKVE 245 TS+ G E L S + LPE+A+ V + S ++ LTFEKGEL A++ E P++AIQK++ Sbjct: 182 TSVGGKETLTSHETLPESAWPTQVSETESRKVELTFEKGELVAIDGEKL-APVRAIQKLQ 240 Query: 246 EIGAAYGIGRDMHVGDTIIGIKGRVGFEAAAPMLIIGAHRFLEKYTLSKWQQYWKDQVAN 305 I +GIGRD+HVGDTIIGIKGRVGFEAA P+LII AH LEK+TL+KWQ WK+Q+++ Sbjct: 241 AIAQPFGIGRDIHVGDTIIGIKGRVGFEAAGPILIIKAHHTLEKHTLTKWQLSWKEQLSS 300 Query: 306 WYGMFLHESQYLEPVMRDIEAMLQESQRNVNGTAILELRPLSFSTVGVESEDDLVKTKFG 365 +YG +LHE Q+ +P+MR+IEA L ++Q+ V+G +EL P F +G+ES DL+ KFG Sbjct: 301 FYGNWLHEGQFHDPIMRNIEAFLADTQKFVSGKVFVELLPYRFQIIGIESNHDLMSNKFG 360 Query: 366 EYGEMQKGWTAEDAKGFIKVTSTPLRVYY 394 YGEM W+ ED KGF K+ + +++ Sbjct: 361 SYGEMNNAWSGEDVKGFSKIFGNQVMIWH 389 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: 474 Number of extensions: 20 Number of successful extensions: 2 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: 395 Length adjustment: 31 Effective length of query: 371 Effective length of database: 364 Effective search space: 135044 Effective search space used: 135044 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 CA265_RS18545 CA265_RS18545 (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.24265.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-85 274.2 0.0 1.3e-85 274.1 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS18545 CA265_RS18545 argininosuccinate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS18545 CA265_RS18545 argininosuccinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 274.1 0.0 1.3e-85 1.3e-85 1 391 [. 3 390 .. 3 393 .. 0.96 Alignments for each domain: == domain 1 score: 274.1 bits; conditional E-value: 1.3e-85 TIGR00032 1 kvvlaysGGlDtsvalklleek.gaeviavtvdvGqp.eedldaieekalklGaekayviDareefvk 66 kvvla+sGGlDts + +l + g+ev +v+v+ G +e+l++ie++a +lG++ + v+D e + + lcl|FitnessBrowser__Pedo557:CA265_RS18545 3 KVVLAFSGGLDTSFCCIYLAQDrGLEVHSVIVNTGGFsDEELQEIEKRAYALGVKSHAVVDETESYYE 70 8************9999998877***********987799**************************** PP TIGR00032 67 dylfaaiqanavyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpd 134 + + n + + +Y+ls + R a+++ + +kk ga+ vahG+tg GnDqvRF++++ +l p+ lcl|FitnessBrowser__Pedo557:CA265_RS18545 71 GCIKYLVFGNVLKNATYPLSVSAERVSQATAIANYVKKIGADYVAHGSTGAGNDQVRFDMIFNILIPE 138 *888899999999999**************************************************** PP TIGR00032 135 lkviaPvreleliReeeieyaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvk 202 +++i+P+r+l+l+Re eiey+a++G+e+ +ek ysi++ l+g s+ ++e + + pe ++ + + lcl|FitnessBrowser__Pedo557:CA265_RS18545 139 VEIITPIRDLKLSREAEIEYLAQHGVEYSAEK-ARYSINKGLWGTSVGGKETLTSHETLPESAWPTQV 205 ******************************97.89**************9988888888888887766 PP TIGR00032 203 dpiektedepevveieFekGvPvalngeslepvelilkaneiagkhGvGriDivEdRiiglKsReiYE 270 + e+ +ve++FekG va++ge+l pv i+k++ ia G+Gr +v d iig+K R +E lcl|FitnessBrowser__Pedo557:CA265_RS18545 206 ---SE--TESRKVELTFEKGELVAIDGEKLAPVRAIQKLQAIAQPFGIGRDIHVGDTIIGIKGRVGFE 268 ...23..35679******************************************************** PP TIGR00032 271 apalllLikAhkdLetlvltkdvlefkeiveekyseliYkGlwfdplaealdalikktqervtGtvrv 338 a++ +l+ikAh+ Le+ +ltk +l +ke ++ y++ + +G ++dp + +++a++ tq+ v+G v v lcl|FitnessBrowser__Pedo557:CA265_RS18545 269 AAGPILIIKAHHTLEKHTLTKWQLSWKEQLSSFYGNWLHEGQFHDPIMRNIEAFLADTQKFVSGKVFV 336 ******************************************************************** PP TIGR00032 339 klfkGnaivigrkseyslYdeelvsfek.dkefdqkdaiGfikirglqikvyre 391 +l +ig +s++ l +++ s+ + +++ + +d +Gf ki g q++++++ lcl|FitnessBrowser__Pedo557:CA265_RS18545 337 ELLPYRFQIIGIESNHDLMSNKFGSYGEmNNAWSGEDVKGFSKIFGNQVMIWHK 390 **************************987999*************999999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (395 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.60 // [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