Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_011371799.1 SUDEN_RS00825 asparagine synthase (glutamine-hydrolyzing)
Query= CharProtDB::CH_005185 (632 letters) >NCBI__GCF_000012965.1:WP_011371799.1 Length = 601 Score = 265 bits (676), Expect = 6e-75 Identities = 194/618 (31%), Positives = 316/618 (51%), Gaps = 33/618 (5%) Query: 1 MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60 MC G+ +H E+ K ++ HRG D G +++ F +LSI + Sbjct: 1 MCAIFGILGEH-------DEKKAKDALALLSHRGGDFCGITQGQNLFFAHHKLSITGTNS 53 Query: 61 -GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAAS 119 QP SYE + FNGEIYNY ELR +L + + F T S+ EV+ A+Y + Sbjct: 54 DSNQPFSYEK--ILLSFNGEIYNYKELRADLSCE-FNFKTQSEAEVIAASYLKWGVNFVL 110 Query: 120 KLRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVYFASERKSLMVAQNDIEIDKE 179 LRGMFA + + D +LY RD G KPL+Y +N + FASE K+L+ + IE+D++ Sbjct: 111 HLRGMFAIALLD--DEILYLFRDRLGKKPLFYLHVNAFI-FASEIKALVPFLHSIEMDED 167 Query: 180 ALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDITFKTYFKA--NFKPVQTEEDKL 237 AL Y+SF P T ++KK+ G ++ I D + K YF + T D+ Sbjct: 168 ALLSYLSFLAPTPPFTFFKNIKKLAAG-EYLIFKDSKVEIKRYFDLLDTTPSLITNRDEA 226 Query: 238 VKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPSLKTFSVGFEQQG-FS 296 V V++A+ +++N+ + +DVP+ S LSGGIDS+ I + AK+ ++T+++G+++ + Sbjct: 227 VFLVQNALEEAINIRLATDVPMASLLSGGIDSAAINAYAKKASMDIQTYTLGYKEFAKYD 286 Query: 297 EVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAKKH- 355 E A +A+ LG++N + IS E+ ++ D+PL DPAA+PLY + KK Sbjct: 287 ERQNASLSASLLGVKNRAVEISQREFDESCDIVLDALDEPLNDPAAVPLYLLFGHIKKDG 346 Query: 356 VTVALSGEGADELFGGYNIYREPLSLKPFERIPSG--LKKMLLHVAAVMPEGMRGKSLLE 413 V LSGEG+DELF GY Y E L ++ + + L ++ E R K + + Sbjct: 347 YKVVLSGEGSDELFLGYRQYFEFLDIEKLTNLKNKNWLSGYFHSNFSMNREWERYKRVFD 406 Query: 414 RGCTPLQDRYIG-NAKIFEESVKKQLLKHYNPNLSYRDVTKTYFTESSSYSDINKMQYVD 472 L R G N +++V + N +L Y + F SS + Y+D Sbjct: 407 GS---LLFRTTGENFTDLQKNVSMKRNVRDNESLKYIQNYRETFLASSHSDESIWYSYID 463 Query: 473 IHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKNGTTKYLLRKAAE 532 +H + L K D+++MA+S+E R PFLD + + I +++ +G TK LL+ A + Sbjct: 464 LHLFQAEHYLTKLDRLSMAHSIESRTPFLDHKLASLVFSIDPKIRYMDGVTKSLLKSALK 523 Query: 533 GIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQTDAYIHKDYVLQLLEDHCADK 592 ++ E +L+R+K GF P +L + ++I+E I K ++L++H Sbjct: 524 PMLDEKILSRRKKGFSNPFMEYL---IESKKISLIKEVNEKTGIFKK---EILDEHIKKA 577 Query: 593 ADNSRK--IWTVLIFMIW 608 A+ K IW + + +W Sbjct: 578 ANGGFKQHIWGLYVLSVW 595 Lambda K H 0.319 0.136 0.403 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: 968 Number of extensions: 55 Number of successful extensions: 9 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: 632 Length of database: 601 Length adjustment: 37 Effective length of query: 595 Effective length of database: 564 Effective search space: 335580 Effective search space used: 335580 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: 53 (25.0 bits)
Align candidate WP_011371799.1 SUDEN_RS00825 (asparagine synthase (glutamine-hydrolyzing))
to HMM TIGR01536 (asnB: asparagine synthase (glutamine-hydrolyzing) (EC 6.3.5.4))
# 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/TIGR01536.hmm # target sequence database: /tmp/gapView.18950.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01536 [M=517] Accession: TIGR01536 Description: asn_synth_AEB: asparagine synthase (glutamine-hydrolyzing) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-123 397.8 0.0 5.6e-123 397.6 0.0 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011371799.1 SUDEN_RS00825 asparagine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011371799.1 SUDEN_RS00825 asparagine synthase (glutamine-hydrolyzing) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 397.6 0.0 5.6e-123 5.6e-123 1 517 [] 2 538 .. 2 538 .. 0.86 Alignments for each domain: == domain 1 score: 397.6 bits; conditional E-value: 5.6e-123 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlseg.aQPlsne 68 C+i+gi+ ++++ +++k l +l+hRG D g+ + +n ++h++L+i+ ++ +QP+s+e lcl|NCBI__GCF_000012965.1:WP_011371799.1 2 CAIFGILGEHDE-----KKAKDALALLSHRGGDFCGITQ---GQNLFFAHHKLSITGTNSDsNQPFSYE 62 9*******9885.....566677889**********744...58**************9988******* PP TIGR01536 69 kevvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137 k ++ fnGEIYN++eLr++l + ++F+t+s +EVi a+y +wg ++v +L+GmFA+al+d+ + l+ lcl|NCBI__GCF_000012965.1:WP_011371799.1 63 K-ILLSFNGEIYNYKELRADLSCE-FNFKTQSEAEVIAASYLKWGVNFVLHLRGMFAIALLDD--EILY 127 *.79******************99.**************************************..**** PP TIGR01536 138 laRDrlGikPLYyaseqgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelepa 206 l+RDrlG+kPL+y ++++faSEiKal+++ e+d++al ++l++ +++ t+fk++k+l ++ lcl|NCBI__GCF_000012965.1:WP_011371799.1 128 LFRDRLGKKPLFYLHV-NAFIFASEIKALVPFL-HSIEMDEDALLSYLSFLAPTPPFTFFKNIKKLAAG 194 **************99.88**************.699**************9999************** PP TIGR01536 207 kal...dgeekleeywevekee..vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslvaa 270 ++l d++ ++++y+++ +++ ++ +e+v ++++le+a++ rl +dvp+++llSGG+DS ++ a lcl|NCBI__GCF_000012965.1:WP_011371799.1 195 EYLifkDSKVEIKRYFDLLDTTpsLITNRDEAVFLVQNALEEAINIRLATDVPMASLLSGGIDSAAINA 263 ***99999999999**9988776777789999************************************* PP TIGR01536 271 iakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptaira 339 akk + +++t+++g+++ +++de + a+ a lg++++ v+is+ e+ + + v+ al+ep++++a lcl|NCBI__GCF_000012965.1:WP_011371799.1 264 YAKKASM-DIQTYTLGYKEFAKYDERQNASLSASLLGVKNRAVEISQREFDESCDIVLDALDEPLNDPA 331 **99976.9************************************************************ PP TIGR01536 340 siplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale...............lpeaselae 393 ++plyll+ ++++g+kVvLsGeG+DElf GY ++e+ e+l + lcl|NCBI__GCF_000012965.1:WP_011371799.1 332 AVPLYLLFGHIKKDGYKVVLSGEGSDELFLGYRQYFEFLDIEKLTnlknknwlsgyfhsnF-------- 392 *************************************999999986667666666555442........ PP TIGR01536 394 kkl.......................llqaklakeselkellkakleeelkekeelkkelkee...sel 436 + l+k++++k+ ++ +e+lk++++ +++ ++ e lcl|NCBI__GCF_000012965.1:WP_011371799.1 393 --SmnrewerykrvfdgsllfrttgeN-FTDLQKNVSMKRNVR--DNESLKYIQNYRETFLASshsDES 456 ..0223333444456677666533321.122222222222222..233334444444444444222444 PP TIGR01536 437 eellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgkeKvlLreaaeel 504 + dl+l+ + + k Dr+smahs+E+R PflD++l++l++si+p+++ dg +K lL++a++ + lcl|NCBI__GCF_000012965.1:WP_011371799.1 457 IWYSYIDLHLFQAEHYLTKlDRLSMAHSIESRTPFLDHKLASLVFSIDPKIRYMDGVTKSLLKSALKPM 525 44568899999888888888************************************************* PP TIGR01536 505 lPeeileRkKeaf 517 l e+il R+K++f lcl|NCBI__GCF_000012965.1:WP_011371799.1 526 LDEKILSRRKKGF 538 **********998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (601 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.03 # Mc/sec: 8.85 // [ok]
This GapMind analysis is from Apr 10 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