Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (characterized)
to candidate WP_024851681.1 N745_RS0108410 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
Query= SwissProt::O06491 (485 letters) >NCBI__GCF_000526715.1:WP_024851681.1 Length = 484 Score = 510 bits (1313), Expect = e-149 Identities = 250/478 (52%), Positives = 338/478 (70%), Gaps = 1/478 (0%) Query: 8 ITELKQLIHKKEIKISDLVDESYKRIQAVDDKVQAFLALDEERARAYAKELDEAVDGRSE 67 I ++ + +H +EI L RI+ D ++ A++++ E A AK+ DE +D + E Sbjct: 6 IRQMSEKLHSREITSVALTQHYLDRIEKYDSELNAYISVTPELAIEMAKKADEMLD-KGE 64 Query: 68 HGLLFGMPIGVKDNIVTKGLRTTCSSKILENFDPIYDATVVQRLQDAEAVTIGKLNMDEF 127 L G+P+ KD G++T+C SK+L NF YDATVV++L+ +GK NMDEF Sbjct: 65 GSFLTGVPVAHKDIFCVDGVKTSCGSKMLHNFVAPYDATVVEKLKAVGMPILGKTNMDEF 124 Query: 128 AMGSSTENSAYKLTKNPWNLDTVPGGSSGGSAAAVAAGEVPFSLGSDTGGSIRQPASFCG 187 AMGSS+E+S Y TKNPWNL+ VPGGSSGGSA+ +AAG P + G+DTGGSIRQPASFCG Sbjct: 125 AMGSSSESSYYGPTKNPWNLNAVPGGSSGGSASVIAAGLAPLATGTDTGGSIRQPASFCG 184 Query: 188 VVGLKPTYGRVSRYGLVAFASSLDQIGPITRTVEDNAFLLQAISGVDKMDSTSANVDVPD 247 + G+KPTYG VSRYG++A+ASS DQ GP+TR+ ED A+LL A++G DK DSTS + + Sbjct: 185 ITGIKPTYGAVSRYGMIAYASSFDQGGPMTRSAEDAAWLLDAMAGFDKKDSTSLEQEKLN 244 Query: 248 FLSSLTGDIKGLKIAVPKEYLGEGVGKEARESVLAALKVLEGLGATWEEVSLPHSKYALA 307 +L+ L ++GLK+ VPKEY GEG+ +V A++VL GA EVSLP+ A+ Sbjct: 245 YLAHLDDSLQGLKVGVPKEYFGEGLSGSVSSAVKEAVEVLRQQGAEIVEVSLPNKDLAVP 304 Query: 308 TYYLLSSSEASANLARFDGIRYGYRTDNADNLIDLYKQTRAEGFGNEVKRRIMLGTFALS 367 YY+L+ +EAS+NL+RFDG+RYGYR +N +L DLY ++R+EGFG EVKRRIM+G +ALS Sbjct: 305 AYYVLAPAEASSNLSRFDGVRYGYRCENPQDLSDLYMRSRSEGFGTEVKRRIMVGAYALS 364 Query: 368 SGYYDAYYKKAQKVRTLIKKDFEDVFEKYDVIVGPTTPTPAFKIGENTKDPLTMYANDIL 427 GYYDAYY KAQK+R +++ DF FEK DVIVGP PT AF IGE + DP++MY D+ Sbjct: 365 EGYYDAYYLKAQKLRRMVRDDFVKAFEKCDVIVGPVAPTTAFNIGEKSDDPISMYLEDLY 424 Query: 428 TIPVNLAGVPGISVPCGLADGLPLGLQIIGKHFDESTVYRVAHAFEQATDHHKAKPEL 485 TIPVNLAG+P +SVP G A+G+P+GL +IG + E+ + VAH F+Q T H+ PE+ Sbjct: 425 TIPVNLAGLPAMSVPAGFAEGMPVGLHLIGTYHSEAKLLNVAHQFQQVTSWHEQMPEV 482 Lambda K H 0.315 0.134 0.381 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: 609 Number of extensions: 19 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: 485 Length of database: 484 Length adjustment: 34 Effective length of query: 451 Effective length of database: 450 Effective search space: 202950 Effective search space used: 202950 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: 52 (24.6 bits)
Align candidate WP_024851681.1 N745_RS0108410 (Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA)
to HMM TIGR00132 (gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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/TIGR00132.hmm # target sequence database: /tmp/gapView.10943.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00132 [M=466] Accession: TIGR00132 Description: gatA: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-196 639.6 0.0 1.8e-196 639.4 0.0 1.0 1 lcl|NCBI__GCF_000526715.1:WP_024851681.1 N745_RS0108410 Asp-tRNA(Asn)/Glu Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000526715.1:WP_024851681.1 N745_RS0108410 Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 639.4 0.0 1.8e-196 1.8e-196 3 464 .. 11 473 .. 9 475 .. 0.99 Alignments for each domain: == domain 1 score: 639.4 bits; conditional E-value: 1.8e-196 TIGR00132 3 ellkkkevsikevleeilerieavkdkinaflevtkekalkkakkldkkva.ke.kklagipiavKdni 69 e+l+++e++++++++++l+rie+ ++++na+++vt+e a+++akk d+ ++ e + l+g+p+a Kd + lcl|NCBI__GCF_000526715.1:WP_024851681.1 11 EKLHSREITSVALTQHYLDRIEKYDSELNAYISVTPELAIEMAKKADEMLDkGEgSFLTGVPVAHKDIF 79 78999*******************************************99965656************* PP TIGR00132 70 avkdiettcaSkiLenyvspydatVverlkeagaliiGktNlDEFamGsstetSafgvtknPeneervp 138 +v +++t+c+Sk+L+n+v+pydatVve+lk+ g+ i+GktN+DEFamGss+e+S++g+tknP+n + vp lcl|NCBI__GCF_000526715.1:WP_024851681.1 80 CVDGVKTSCGSKMLHNFVAPYDATVVEKLKAVGMPILGKTNMDEFAMGSSSESSYYGPTKNPWNLNAVP 148 ********************************************************************* PP TIGR00132 139 GGSsgGsaaavaadlvplalgsDTGgSiRqPAsfcgvvGlKPtYGlvSRyGlvayasSldqiGilakkv 207 GGSsgGsa ++aa+l+pla g+DTGgSiRqPAsfcg+ G+KPtYG+vSRyG++ayasS+dq G+++++ lcl|NCBI__GCF_000526715.1:WP_024851681.1 149 GGSSGGSASVIAAGLAPLATGTDTGGSIRQPASFCGITGIKPTYGAVSRYGMIAYASSFDQGGPMTRSA 217 ********************************************************************* PP TIGR00132 208 edialvldvisgkDkkDstslevkveelleelkkdlkglkvgvvkelseesldkevkekfeklleklee 276 ed+a +ld+++g DkkDstsle ++ ++l +l + l+glkvgv ke+++e+l+ +v++++++++e+l++ lcl|NCBI__GCF_000526715.1:WP_024851681.1 218 EDAAWLLDAMAGFDKKDSTSLEQEKLNYLAHLDDSLQGLKVGVPKEYFGEGLSGSVSSAVKEAVEVLRQ 286 ********************************************************************* PP TIGR00132 277 lgaeivevslpsvklalaiYyiispsEassnlarydgiryGkrveelkslkelyaktRsegfgeevkrR 345 +gaeivevslp+ +la+++Yy+++p+Eassnl+r+dg+ryG+r e++++l++ly+++Rsegfg+evkrR lcl|NCBI__GCF_000526715.1:WP_024851681.1 287 QGAEIVEVSLPNKDLAVPAYYVLAPAEASSNLSRFDGVRYGYRCENPQDLSDLYMRSRSEGFGTEVKRR 355 ********************************************************************* PP TIGR00132 346 imlGayalskeyydkyykkAqkvrtliidefeklfeevDvivsptaptlafklgekaedplemylsDvl 414 im+Gayals++yyd+yy+kAqk+r++++d+f k+fe++Dviv+p+apt+af++gek +dp++myl+D++ lcl|NCBI__GCF_000526715.1:WP_024851681.1 356 IMVGAYALSEGYYDAYYLKAQKLRRMVRDDFVKAFEKCDVIVGPVAPTTAFNIGEKSDDPISMYLEDLY 424 ********************************************************************* PP TIGR00132 415 tvpanlaGlpaisvPlgkkekglpiGlqiigkafddkkllsvakaleqal 464 t+p+nlaGlpa+svP+g + +g+p+Gl +ig + ++ kll+va++++q + lcl|NCBI__GCF_000526715.1:WP_024851681.1 425 TIPVNLAGLPAMSVPAGFA-EGMPVGLHLIGTYHSEAKLLNVAHQFQQVT 473 *******************.7*************************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (484 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: 00:00:00.01 # Mc/sec: 12.53 // [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