Align asparagine synthase (glutamine-hydrolysing) 1; EC 6.3.5.4 (characterized)
to candidate WP_027458901.1 K420_RS0115800 amidotransferase 1, exosortase A system-associated
Query= CharProtDB::CH_005185 (632 letters) >NCBI__GCF_000519045.1:WP_027458901.1 Length = 635 Score = 336 bits (862), Expect = 2e-96 Identities = 207/626 (33%), Positives = 337/626 (53%), Gaps = 28/626 (4%) Query: 1 MCGFVGVFNKHPLAQTADQEELIKQMNQMIVHRGPDSDGYFHDEHVGFGFRRLSIIDVEN 60 MCG G+F+ ++ ++ +MN+ HRGPD G + +G G RRLSIID+ Sbjct: 1 MCGITGIFDTR--SRRDIDRAVLHRMNEAQFHRGPDEGGLHIEPGLGLGHRRLSIIDLST 58 Query: 61 GGQPLSYEDETYWIIFNGEIYNYIELREELEAKGYTFNTDSDTEVLLATYRHYKEEAASK 120 G QPL ED++ ++FNGEIYNY EL EL+A G+ F+T SDTEV++ + + E + Sbjct: 59 GQQPLYNEDKSVCVVFNGEIYNYQELIPELQALGHVFHTRSDTEVIVHAWEAWGERCVDR 118 Query: 121 LRGMFAFLIWNKNDHVLYGARDPFGIKPLYYTTINDQVY-FASERKSLMVAQN-DIEIDK 178 RGMFAF +W++N L+ ARD G+KPL+Y ++D + F SE KSL+ +ID Sbjct: 119 FRGMFAFALWDRNRETLFLARDRLGVKPLFYALLDDGSFLFGSELKSLLAHGGLKRDIDP 178 Query: 179 EALQQYMSFQFVPEPSTLDAHVKKVEPGSQFTIRPDGDI-TFKTYFKANF---KPVQTEE 234 A+++Y + +V EP + +K+ P +R + + Y+ F P+ + Sbjct: 179 CAVEEYFALGYVAEPRAIFKQARKLPPACTLLLRRGQPVGQPREYWDVRFTLDNPISDAD 238 Query: 235 DKLVKEVRDAIYDSVNVHMRSDVPVGSFLSGGIDSSFIVSVAKEFHPS-LKTFSVGFEQQ 293 + E+ + +S+ + M S+VP+G+FLSGG+DSS +V++ + + T S+GF Sbjct: 239 AQ--AELTHRLEESIKLRMISEVPLGAFLSGGVDSSAVVAMMAGLSANPVNTCSIGFSDP 296 Query: 294 GFSEVDVAKETAAALGIENISKVISPEEYMNELPKIVWHFDDPLADPAAIPLYFVAKEAK 353 F+E + A+ A + V+ +++ + + + +D+P AD +AIP Y V + A+ Sbjct: 297 AFNESEFARMVADRYHTNHHLDVVESDDF-DLIDTLARLYDEPYADSSAIPTYRVCQLAR 355 Query: 354 KHVTVALSGEGADELFGGYNIYR-EPLSLKPFERIPSGLKKMLLHVAAVM-------PEG 405 KHVTVALSG+G DE FGGY Y+ + K +P GL++ L + P Sbjct: 356 KHVTVALSGDGGDESFGGYRRYKLHLMEEKMRSALPLGLRRPLFGTLGKLYPKADWAPRV 415 Query: 406 MRGKSLLERGCTPLQDRYIGNAKIFEESVKKQLLK-HYNPNLSYRDVTKTYFTESSSYSD 464 R K+ E + Y + I ++ QL + L D + FT+ ++ +D Sbjct: 416 FRAKTTFEGIARSSVEGYFHSVSILRAPMRNQLFSPQFKAALGGYDALQV-FTDHAAKAD 474 Query: 465 ----INKMQYVDIHTWMRGDILLKADKMTMANSLELRVPFLDKVVFDVASKIPDELKTKN 520 + +QY+D+ T++ GDI K D+ +MA+SLE+R P +D + + + +P K + Sbjct: 475 TQDPLALIQYLDLKTYLIGDINTKVDRASMAHSLEVREPLMDHKLVEWLATLPSTQKIRG 534 Query: 521 GTTKYLLRKAAEGIVPEHVLNRKKLGFPVPIRHWLKNEMNEWVRNIIQESQ--TDAYIHK 578 KYLL+KA E +P VL R K+GF VP+ W + + V+ I S+ + ++ Sbjct: 535 QEGKYLLKKAMEPHLPNDVLYRPKMGFSVPLARWFRGPLKARVQESILGSRLADTGWFNR 594 Query: 579 DYVLQLLEDHCADKADNSRKIWTVLI 604 DY+ +L+ DH D S IWT+L+ Sbjct: 595 DYLQELVRDHNNGNRDYSASIWTILM 620 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: 982 Number of extensions: 48 Number of successful extensions: 7 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: 635 Length adjustment: 38 Effective length of query: 594 Effective length of database: 597 Effective search space: 354618 Effective search space used: 354618 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: 54 (25.4 bits)
Align candidate WP_027458901.1 K420_RS0115800 (amidotransferase 1, exosortase A system-associated)
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.597.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-152 494.3 0.0 3e-152 494.1 0.0 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027458901.1 K420_RS0115800 amidotransferase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027458901.1 K420_RS0115800 amidotransferase 1, exosortase A system-associated # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 494.1 0.0 3e-152 3e-152 1 517 [] 2 561 .. 2 561 .. 0.92 Alignments for each domain: == domain 1 score: 494.1 bits; conditional E-value: 3e-152 TIGR01536 1 CgiagivdlkakakeeeeaikemletlahRGPDaegvwkdekeenailghrRLaiidlsegaQPlsnek 69 Cgi+gi+d + + +++ +++m+e++ hRGPD+ g++++ + +lghrRL+iidls+g+QPl+ne+ lcl|NCBI__GCF_000519045.1:WP_027458901.1 2 CGITGIFDTRSRRDIDRAVLHRMNEAQFHRGPDEGGLHIE---PGLGLGHRRLSIIDLSTGQQPLYNED 67 *********98877799********************999...7************************* PP TIGR01536 70 .evvivfnGEIYNheeLreeleekGyeFetksDtEViLaayeewgeelverLeGmFAfalwdekkgelf 137 +v +vfnGEIYN++eL el++ G+ F+t+sDtEVi++a+e+wge++v+r++GmFAfalwd+++++lf lcl|NCBI__GCF_000519045.1:WP_027458901.1 68 kSVCVVFNGEIYNYQELIPELQALGHVFHTRSDTEVIVHAWEAWGERCVDRFRGMFAFALWDRNRETLF 136 999****************************************************************** PP TIGR01536 138 laRDrlGikPLYyase.qgkllfaSEiKallalkeikaeldkealaelltlqlvptektlfkevkelep 205 laRDrlG+kPL+ya +g++lf+SE+K+lla+ k+ +d a+ e+++l +v++++ +fk+ ++l+p lcl|NCBI__GCF_000519045.1:WP_027458901.1 137 LARDRLGVKPLFYALLdDGSFLFGSELKSLLAHGGLKRDIDPCAVEEYFALGYVAEPRAIFKQARKLPP 205 **************8779*************************************************** PP TIGR01536 206 akal.....dgeekleeywevekee.vkeseeelveelrelledavkkrlvadvpvgvllSGGlDSslv 268 a l ++ + +eyw+v+ + s+ ++ +el + le+++k r++++vp+g++lSGG+DSs+v lcl|NCBI__GCF_000519045.1:WP_027458901.1 206 ACTLllrrgQPVGQPREYWDVRFTLdNPISDADAQAELTHRLEESIKLRMISEVPLGAFLSGGVDSSAV 274 *9999998888888888*****99866678899999********************************* PP TIGR01536 269 aaiakkeaksevktFsigfedskdldeskaarkvadelgtehkevliseeevlkeleevilaleeptai 337 +a+++ ++++v+t sigf +++++es++ar vad t+h+ ++++++ ++ ++ + + +ep a+ lcl|NCBI__GCF_000519045.1:WP_027458901.1 275 VAMMAGLSANPVNTCSIGFS-DPAFNESEFARMVADRYHTNHHLDVVESDD-FDLIDTLARLYDEPYAD 341 ********************.**********************99988888.599************** PP TIGR01536 338 rasiplyllsklarekgvkVvLsGeGaDElfgGYeyfreakaeeale...................... 384 +++ip+y +++lar++ v+V+LsG+G+DE fgGY +++ +ee+++ lcl|NCBI__GCF_000519045.1:WP_027458901.1 342 SSAIPTYRVCQLARKH-VTVALSGDGGDESFGGYRRYKLHLMEEKMRsalplglrrplfgtlgklypka 409 ****************.******************************9*99999999999999998886 PP TIGR01536 385 ..........lpeaselaekkl............llqaklakeselkellkakleeelkekeelkkelk 431 + + +++ ++ ++ ++l++ +++++l ++l+ + lcl|NCBI__GCF_000519045.1:WP_027458901.1 410 dwaprvfrakT----------TfegiarssvegyFHSVSILRAPMRNQLFSPQFKAALGGYDALQVFTD 468 66333322220..........134556666677788888888888888888888877655444333222 PP TIGR01536 432 ee......seleellrldlelllsdllrak.DrvsmahslEvRvPflDkelvelalsippelklrdgke 493 ++ l+ +++ldl+++l ++++ k Dr+smahslEvR P++D++lve +++p k+r ++ lcl|NCBI__GCF_000519045.1:WP_027458901.1 469 HAakadtqDPLALIQYLDLKTYLIGDINTKvDRASMAHSLEVREPLMDHKLVEWLATLPSTQKIRGQEG 537 22234455999********************************************************** PP TIGR01536 494 KvlLreaaeellPeeileRkKeaf 517 K+lL++a+e +lP+++l+R+K++f lcl|NCBI__GCF_000519045.1:WP_027458901.1 538 KYLLKKAMEPHLPNDVLYRPKMGF 561 **********************99 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (517 nodes) Target sequences: 1 (635 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: 11.77 // [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