Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF2939 HP15_2883 glutamyl-tRNA (Gln) amidotransferase subunit A
Query= curated2:O83983 (506 letters) >FitnessBrowser__Marino:GFF2939 Length = 604 Score = 192 bits (487), Expect = 4e-53 Identities = 161/487 (33%), Positives = 221/487 (45%), Gaps = 53/487 (10%) Query: 29 VRAFRNVYEEDTRSASPLGALVEFFSDAEE------HARTADNLRASCAQSTKTAGANGG 82 +R ++ Y+E S LG L+ + + D A Q + AG G Sbjct: 6 IRDWQQAYKEGATPESLLGELLTGLDTTDVAWISLLDQKGLDEALAGLKQKLQDAG---G 62 Query: 83 SVSGKPLLGLPFAVKDNISVKGKHCTCGSKLLADYRAPYDATVVARLRAAGAIPLGRTNM 142 + PL G+PFA KDNI G T A Y DAT VARL+AAGAI +G+TN+ Sbjct: 63 EIDKLPLYGIPFAAKDNIDAVGFETTAACPAFA-YTPEEDATTVARLKAAGAIVIGKTNL 121 Query: 143 DEFAMGSSTEYSVYGPTRNPRDRSRTSGGSSGGSAAAVAGGQAPFALGTETGGSVRLPAA 202 D+FA G S YG N SGGSS GSA+ VA G APFALGT+T GS R+PA Sbjct: 122 DQFATGLVGTRSPYGAVPNSFKPDVVSGGSSSGSASVVARGLAPFALGTDTAGSGRVPAG 181 Query: 203 YCGLYGLKPTYGLLSRYGVVAFGSSLDQIGFFATCIDDIALALSVTSGKDLYDSTSTCPP 262 L GLKPT GL S GVV SLD + FA ++D L +G D D+ S PP Sbjct: 182 LNNLVGLKPTKGLFSIRGVVPACRSLDCVSIFALTVNDAGLVSDTMAGFDADDAFSRKPP 241 Query: 263 PATGRHAVSHHLAPFSAHECSILRAAVPRELVDAPGVHPDVSAQ--FQRFLTWLRAQNVQ 320 A P I R A+P D P D A+ + ++ R QNV+ Sbjct: 242 YALPLD------GPALRRPGPIQRLAIP----DHPQWFGDQQAEAAWNTAISQWRQQNVE 291 Query: 321 VEEVTL-PALQAAVPVYYLVATAEAASNLARFDGIRYGQRGDTDALLENYYRAVRTSGFG 379 + + P L+ A +Y AE + + F GD Sbjct: 292 LVPLDFSPMLELAALLYEGPWVAERHAAVESF----MTSHGD---------------DMN 332 Query: 380 PEVQRRII-VGNYVLSRHFSGDYYRTSVRVRSRIEQECTQLLCSYHFIVCPTAATGAFPL 438 P V+ I GN+ + F Y + ++++ +LL ++ PTA T P Sbjct: 333 PVVKGIISKAGNFSATDTFKAQYR------KEELQRQIDELLADVDALLVPTAPTA--PT 384 Query: 439 GERIH-DPLAMYCS-DLFTTFVNLARLPALSVPVGTSGTGLPIGIQIIGSQWQECAVLRL 496 E ++ DP+A+ +T FVNLA + AL++P G GLP G+ +I W++ + RL Sbjct: 385 IEAVNADPVALNSQLGTYTNFVNLADMSALAIPAGFRDDGLPFGVTLISGAWKDTELQRL 444 Query: 497 AKRWEEA 503 A +W A Sbjct: 445 ACQWLNA 451 Lambda K H 0.320 0.134 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: 799 Number of extensions: 39 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 506 Length of database: 604 Length adjustment: 36 Effective length of query: 470 Effective length of database: 568 Effective search space: 266960 Effective search space used: 266960 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 (21.8 bits) S2: 53 (25.0 bits)
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