Align argininosuccinate synthase (EC 6.3.4.5) (characterized)
to candidate 5207683 Shew_0205 argininosuccinate synthase (RefSeq)
Query= BRENDA::A4I066 (418 letters) >FitnessBrowser__PV4:5207683 Length = 407 Score = 418 bits (1075), Expect = e-121 Identities = 209/395 (52%), Positives = 270/395 (68%), Gaps = 3/395 (0%) Query: 15 RVVLAYSGGLDTSVIIPWLKENYDY-EVIACCANVGQGAGEIDGLEEKAKKSGASKLYLL 73 +VVLAYSGGLDTS IIPWLKE YD E++A CA+VGQG E++GL EKA SGAS+ Y++ Sbjct: 12 KVVLAYSGGLDTSAIIPWLKETYDNCEIVAFCADVGQGEAELEGLHEKAIASGASECYIV 71 Query: 74 DLREEYVTDYIFPTLKAGATYEGKYMLGTSHARPLIAKHLVEVAHKEGAVAICHGATGKG 133 DL+EE V DYI+PT+ GA YEG Y+LGTS ARP+IAK VEVA K GA A+CHG TGKG Sbjct: 72 DLKEELVADYIYPTIATGAIYEGTYLLGTSMARPIIAKAQVEVARKVGADAVCHGCTGKG 131 Query: 134 NDQVRFELAVMALDPSLKCVAPWREWNIKSREDAIDYAEAHGVPVPCTKSDLYSRDRNLW 193 NDQVRFE AL P L +APWREW++ SRED +DY + + + +YSRD N W Sbjct: 132 NDQVRFEGCFAALAPDLTVIAPWREWSMVSREDLLDYLAERNIKTTASATKIYSRDANAW 191 Query: 194 HISHEGMDLEDPANEPAYARLLRLCNTVEKAPDEAEYVTVQFEKGIPVAVNGRKMSSVEL 253 HISHEG +LEDP NEP+ + + E APDE EYV+V+ E G VNG+ + Sbjct: 192 HISHEGGELEDPWNEPS-KEVWTMTVAPEDAPDEPEYVSVEMEAGRITKVNGQSYTPYGA 250 Query: 254 VEELNALGGKHAIGIEDIVEDRLVGMKSRGVYETPAGTILYKALDMLESLCLDRDTQSFK 313 + LN + G H +G DI E+RLVGMKSRG YETP GT+++ AL +E L LD+ ++ ++ Sbjct: 251 LMALNEIAGAHGVGRIDITENRLVGMKSRGCYETPGGTVMFAALRAIEELVLDKTSREWR 310 Query: 314 RQSAVRFSELVYDGKWFTPLRESMSAMFDQMAETVTGEATLKLYKGNLVPAGAQSPYSLY 373 Q + + LVYDG+WFTPL ES+ +A + GE LKLYKG +SP SLY Sbjct: 311 EQVGAKMAHLVYDGRWFTPLCESLLGASQPLANLLNGEVVLKLYKGQAQAVKKRSPNSLY 370 Query: 374 NKNIASFGDSQHLYNHHDAEGFIRLFGLPLRVRSM 408 ++ A+FG+ + +YN DAEGFIRL+ L R+R++ Sbjct: 371 SEEFATFGEDE-VYNQKDAEGFIRLYSLASRIRAL 404 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: 479 Number of extensions: 16 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: 407 Length adjustment: 31 Effective length of query: 387 Effective length of database: 376 Effective search space: 145512 Effective search space used: 145512 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 5207683 Shew_0205 (argininosuccinate synthase (RefSeq))
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.12442.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-142 458.9 0.0 1e-141 458.7 0.0 1.0 1 lcl|FitnessBrowser__PV4:5207683 Shew_0205 argininosuccinate synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5207683 Shew_0205 argininosuccinate synthase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.7 0.0 1e-141 1e-141 1 388 [. 12 401 .. 12 407 .] 0.98 Alignments for each domain: == domain 1 score: 458.7 bits; conditional E-value: 1e-141 TIGR00032 1 kvvlaysGGlDtsvalklleek..gaeviavtvdvGqpeedldaieekalklGaekayviDareefvkdylfaaiqan 76 kvvlaysGGlDts+++++l+e ++e++a+++dvGq+e++l+ +eka++ Ga + y++D +ee+v+dy+ ++i ++ lcl|FitnessBrowser__PV4:5207683 12 KVVLAYSGGLDTSAIIPWLKETydNCEIVAFCADVGQGEAELEGLHEKAIASGASECYIVDLKEELVADYIYPTIATG 89 8********************98788**************************************************** PP TIGR00032 77 avyegkYllstaLaRpliakklvevakkegaeavahGctgKGnDqvRFelsilllnpdlkviaPvreleli.Reeeie 153 a+yeg+Yll+t++aRp+iak++veva+k ga+av hGctgKGnDqvRFe + +l+pdl viaP+re+ ++ Re++++ lcl|FitnessBrowser__PV4:5207683 90 AIYEGTYLLGTSMARPIIAKAQVEVARKVGADAVCHGCTGKGNDQVRFEGCFAALAPDLTVIAPWREWSMVsREDLLD 167 *********************************************************************998****** PP TIGR00032 154 yaaekGievpvekekaysiDenllgrsiEageLEdpsteppediyelvkdpiektedepevveieFekGvPvalnges 231 y+ae+ i++ ++ k ys D n +++s+E+geLEdp+ ep ++++++++ p++++ depe+v +e e G ++ng+s lcl|FitnessBrowser__PV4:5207683 168 YLAERNIKTTASATKIYSRDANAWHISHEGGELEDPWNEPSKEVWTMTVAPEDAP-DEPEYVSVEMEAGRITKVNGQS 244 *************************************************887777.********************** PP TIGR00032 232 lepvelilkaneiagkhGvGriDivEdRiiglKsReiYEapalllLikAhkdLetlvltkdvlefkeiveekyseliY 309 ++p + ++neiag+hGvGriDi E+R++g+KsR++YE+p+ +++ A +++e+lvl+k +e++e v+ k+++l+Y lcl|FitnessBrowser__PV4:5207683 245 YTPYGALMALNEIAGAHGVGRIDITENRLVGMKSRGCYETPGGTVMFAALRAIEELVLDKTSREWREQVGAKMAHLVY 322 ****************************************************************************** PP TIGR00032 310 kGlwfdplaealdalikktqervtGtvrvklfkGnaivigrkseyslYdeelvsfekdkefdqkdaiGfikirglqik 387 G+wf pl+e l + + ++ ++G+v +kl+kG+a + ++s++slY+ee ++f +d+ ++qkda+Gfi++++l + lcl|FitnessBrowser__PV4:5207683 323 DGRWFTPLCESLLGASQPLANLLNGEVVLKLYKGQAQAVKKRSPNSLYSEEFATFGEDEVYNQKDAEGFIRLYSLASR 400 *************************************************************************99876 PP TIGR00032 388 v 388 + lcl|FitnessBrowser__PV4:5207683 401 I 401 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (407 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: 12.10 // [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