Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate Echvi_3042 Echvi_3042 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit
Query= SwissProt::Q9RF06 (475 letters) >FitnessBrowser__Cola:Echvi_3042 Length = 487 Score = 417 bits (1073), Expect = e-121 Identities = 217/477 (45%), Positives = 312/477 (65%), Gaps = 6/477 (1%) Query: 3 FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62 +E V+GLEVHV+L T SKM++ FG PN+N +VI L +PG LP VNKRAV++AM+ Sbjct: 10 YELVVGLEVHVQLLTKSKMYASDSTEFGNLPNTNISVITLGHPGTLPKVNKRAVEFAMKL 69 Query: 63 AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDI--EVDGETKRIGITR 120 +A EI + F RKNYFYPD PK YQ++Q P+ G + I E G T+ I +TR Sbjct: 70 GLACKSEITRHNIFARKNYFYPDLPKGYQLTQDKNPVCVGGTVPITLEKSGVTREIELTR 129 Query: 121 LHMEEDAGKSTH-KGEY-SLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTG 178 +HMEEDAGKS H GE +LVD NR G PL+EIV+EP IR+ +EAY ++ ++R +++Y Sbjct: 130 IHMEEDAGKSMHLAGEVDTLVDFNRAGVPLLEIVTEPCIRASEEAYQFMSEIRKLVRYLE 189 Query: 179 VSDVKMEEGSLRCDANISLRPYGQEKFGTKAELKNLNSFNYVRKGLEYEEKRQEEELLSG 238 + D MEEGS+RCDANIS+R G + G K E+KN+NSF V + +E+E RQ + + G Sbjct: 190 ICDGNMEEGSMRCDANISIRLKGDTELGKKVEVKNMNSFRNVARAIEHEFDRQIDMMEKG 249 Query: 239 GEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVRQTIPELPDE 298 I ETR FD +TG T MR KE +DYRYFPEPD+ P+ I D W +++ +++P LP E Sbjct: 250 ETIISETRTFDATTGLTAGMRTKEDLNDYRYFPEPDLSPVVISDEWLQQISESMPSLPRE 309 Query: 299 RKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVNEYLNKNQVE 358 ++VN GLP YDA+VLT +KE++ +FE+ + K SNW+MG V YLN+ + Sbjct: 310 LHERFVNAFGLPEYDANVLTDSKEIALYFEALCGETNNYKAASNWMMGPVKSYLNELTLH 369 Query: 359 LLDTKLTPENLAGMIKLIEDGTMSSKIA-KKVFPELAAKGGNAK-QIMEDNGLVQISDEA 416 + D + P+ LA +I LI++G ++ +A +KV+PE+ + +I + L+Q SDE Sbjct: 370 IEDFPVRPKQLASLIALIDEGKVNFSVASQKVYPEMIKDPSQSPLEIAQKLNLIQESDEG 429 Query: 417 TLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLKQELD 473 +L V L NE V +YK+GK +G +GQ+MK SKG+A+P++ N++L + L+ Sbjct: 430 SLKPIVESVLAENEAKVAEYKSGKKGLLGMFMGQVMKKSKGKADPKVANKILTELLE 486 Lambda K H 0.313 0.133 0.373 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: 652 Number of extensions: 27 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: 475 Length of database: 487 Length adjustment: 34 Effective length of query: 441 Effective length of database: 453 Effective search space: 199773 Effective search space used: 199773 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 bits)
Align candidate Echvi_3042 Echvi_3042 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))
# 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/TIGR00133.hmm # target sequence database: /tmp/gapView.5398.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00133 [M=481] Accession: TIGR00133 Description: gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-170 553.9 0.1 1.5e-170 553.7 0.1 1.0 1 lcl|FitnessBrowser__Cola:Echvi_3042 Echvi_3042 aspartyl/glutamyl-tRN Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_3042 Echvi_3042 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 553.7 0.1 1.5e-170 1.5e-170 3 480 .. 9 485 .. 7 486 .. 0.97 Alignments for each domain: == domain 1 score: 553.7 bits; conditional E-value: 1.5e-170 TIGR00133 3 eyelviGlEvHvqlntksKlFckcsneaqeakpNtnvcpvclglPGalPvlNkeavkkAlklalalnskivsev 76 +yelv+GlEvHvql tksK++++ s+e+ + pNtn++ + lg PG+lP +Nk+av++A+kl+la +s+i+ lcl|FitnessBrowser__Cola:Echvi_3042 9 KYELVVGLEVHVQLLTKSKMYASDSTEFGN-LPNTNISVITLGHPGTLPKVNKRAVEFAMKLGLACKSEIT-RH 80 79****************************.9*************************************66.69 PP TIGR00133 77 svFdRKhYfYpDlPkgyqitqqdlPiaedGkleieleeke..keigierlhlEeDtgksqykesdkdkqslvDf 148 +F+RK+YfYpDlPkgyq+tq + P++ +G++ i le++ +ei+++r+h+EeD+gks++ ++ +lvDf lcl|FitnessBrowser__Cola:Echvi_3042 81 NIFARKNYFYPDLPKGYQLTQDKNPVCVGGTVPITLEKSGvtREIELTRIHMEEDAGKSMHLAG--EVDTLVDF 152 9******************************98776665455********************66..589***** PP TIGR00133 149 NRsgvPLlEiVtkPdlksakearaflkklrqilryleisdgdleeGsmRvDvNvsirlkGqekegtrvEiKNln 222 NR+gvPLlEiVt+P ++ ++ea +f++++r+++rylei dg++eeGsmR+D+N+sirlkG+++ g++vE+KN+n lcl|FitnessBrowser__Cola:Echvi_3042 153 NRAGVPLLEIVTEPCIRASEEAYQFMSEIRKLVRYLEICDGNMEEGSMRCDANISIRLKGDTELGKKVEVKNMN 226 ************************************************************************** PP TIGR00133 223 slksiekaieyEieRqkkllkkgeevkqetrafdekksitvslRkKeeseDYRYfpePdlppieideevvkekv 296 s++++++aie+E Rq+++++kge++ etr+fd ++ t +R Ke+ +DYRYfpePdl p++i++e++++ + lcl|FitnessBrowser__Cola:Echvi_3042 227 SFRNVARAIEHEFDRQIDMMEKGETIISETRTFDATTGLTAGMRTKEDLNDYRYFPEPDLSPVVISDEWLQQ-I 299 *********************************************************************999.* PP TIGR00133 297 eeklpelPeakrirlkkeyglseedakvlvsdlelldafeevvklikepklavnWileellgeLnkkkislaea 370 +e +p lP++ ++r+++ +gl e+da+vl++ +e++ +fe + +++ k+a nW++ ++++Ln+ ++ ++++ lcl|FitnessBrowser__Cola:Echvi_3042 300 SESMPSLPRELHERFVNAFGLPEYDANVLTDSKEIALYFEALCGETNNYKAASNWMMGPVKSYLNELTLHIEDF 373 ************************************************************************** PP TIGR00133 371 llkpeelaeliklikegkisqksa.kelleellen.kkdpkklieklgliqisdekelvkiveevikenpkeve 442 ++p++la+li+li+egk++ a +++ e++++ ++p ++++kl+liq sde l+ ive v++en+ +v lcl|FitnessBrowser__Cola:Echvi_3042 374 PVRPKQLASLIALIDEGKVNFSVAsQKVYPEMIKDpSQSPLEIAQKLNLIQESDEGSLKPIVESVLAENEAKVA 447 ********************8876267999999988999*********************************** PP TIGR00133 443 kyksgkekalkflvGqvmkktkgradpkevekllkell 480 +yksgk+ +l++++Gqvmkk+kg+adpk ++k+l ell lcl|FitnessBrowser__Cola:Echvi_3042 448 EYKSGKKGLLGMFMGQVMKKSKGKADPKVANKILTELL 485 ************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (481 nodes) Target sequences: 1 (487 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: 10.22 // [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