Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF2509 PGA1_c25470 putative glutamyl-tRNA(Gln) amidotransferase subunit A
Query= curated2:Q6MRL7 (490 letters) >FitnessBrowser__Phaeo:GFF2509 Length = 468 Score = 201 bits (510), Expect = 6e-56 Identities = 159/484 (32%), Positives = 244/484 (50%), Gaps = 48/484 (9%) Query: 5 FASLSEISEAVNNRSISAKE-VTLHFLKRIENLNPKLNAFTSLNPQ-AVQEAEAVDARIA 62 FAS +++ A+ ++IS++E VTLH L+ I +NP +NA +L + A++EA+ DA+IA Sbjct: 6 FASAVQMAAALQRKTISSRELVTLH-LEHISVVNPAINAIVTLAAERALEEAQVTDAQIA 64 Query: 63 NGEDVGLLAGVPFGIKEMFCTKGLTTTAGSKILENFVPPYDATAVARLKKSGIVVMGKLN 122 G G L GVP IK+ F T+G+ +T G FVP DAT VARL+K+G +V+GK N Sbjct: 65 QGRFSGPLMGVPVTIKDSFDTEGIVSTYGMAARAGFVPNRDATVVARLRKAGAIVLGKTN 124 Query: 123 QDEFAMGSSNETS--FHGVVKNPWDLERVPGGSSGGSAAAQASRLVAGTLGTDTGGSIRQ 180 E + T+ HG NP D R P GSSGG+AAA A+ A +G+DTGGSIR Sbjct: 125 TSELTAHRAEHTNPPLHGRTNNPHDFARSPSGSSGGAAAAVAAGCAALDIGSDTGGSIRD 184 Query: 181 PASFCGIVGVKPTYGRVSRYG-IVAYA----SSLDQAGPMVSSVRDAALTLEVISGFDPQ 235 PA CG+VG+KP+ G V R G V+Y L Q GPM V D +L L VISG D Sbjct: 185 PAHVCGVVGIKPSAGLVPRTGHCVSYGLGTLDLLTQVGPMARYVEDVSLALSVISGPDGN 244 Query: 236 DSTTTQKQVPAWSQNLK-ADVKGMKIGLMKEYMTGALDPDVQKTVENSVDTLKQLGAEIV 294 D +S N++ D+ G+++ + + D K V ++ L+ A ++ Sbjct: 245 DLDANS----VYSCNIEDVDLAGLRVAYYTDSGAHQVSDDATKAVISAAAALQDAKA-VL 299 Query: 295 EVSVPMTAFAVPVYYLVAASEASSNLSRYDGVKYGYRAEFKNLSAVDLEEFYSQTRGQAF 354 P F AS+ L DG + + + + RG Sbjct: 300 RQDFPACLF--------DASKLFEALVSVDGGLWKHELAKRAI------------RGGTA 339 Query: 355 GAEVKRRIMLGTYCLS-SGYYDAFYNKAGQVRRLIMEQYLEAFKKCDVILSPVTTAPAFK 413 G+ R++M L+ AF + G + + + Y+E K D +L PV+ A Sbjct: 340 GS---RKLMPQLSALAPDSTVTAFGKRIGPFKAGLAD-YME---KYDALLGPVSPQAARL 392 Query: 414 IGERVSDPLAMYLNDIFTTSTNLAGLPGMSVPFGQSQSGLPIGIQLTAGHFEEQKMLNVA 473 + + N++ ++ NL+G P ++VP ++ +GLP+G+Q+ + + L VA Sbjct: 393 HADTPQG--YSFWNEL--SAHNLSGFPAVTVPAARTSNGLPVGVQIVSTAGRDHVALAVA 448 Query: 474 FALE 477 A++ Sbjct: 449 KAIQ 452 Lambda K H 0.316 0.132 0.372 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: 479 Number of extensions: 24 Number of successful extensions: 5 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: 490 Length of database: 468 Length adjustment: 34 Effective length of query: 456 Effective length of database: 434 Effective search space: 197904 Effective search space used: 197904 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: 51 (24.3 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