Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012334347.1 M446_RS22140 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000019365.1:WP_012334347.1 Length = 473 Score = 254 bits (649), Expect = 5e-72 Identities = 171/483 (35%), Positives = 246/483 (50%), Gaps = 37/483 (7%) Query: 7 LTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARRAAG 66 ++ A +A +S ++ +ALL RI +EP++ AF+ V AA AR A A+ +G Sbjct: 19 MSAASLARAIAARRLSPVDAVEALLARIDRLEPRLHAFVEVYAADARLAAEGAERAIRSG 78 Query: 67 DA-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLNCD 125 A PL G+P+ +KD+I +G +T S AT R+ A G ++LGK + Sbjct: 79 HAVGPLHGVPVALKDLIDVEGRISTGGSMTRRVQRATASATVAKRMIAQGMILLGKTHTV 138 Query: 126 EFAMGSSTENSAFQQTRNPWN--LERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPA 183 EFA G N NPW+ RVPGGSS GS AVA+ AP A+GTDTGGS+R PA Sbjct: 139 EFAFGGWGTNQHMGTPLNPWDPARPRVPGGSSSGSGVAVASRMAPWAIGTDTGGSVRLPA 198 Query: 184 ALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDY 243 + CGITGLK T GRVS G++ +++LD GPMAR+V D A++ V+ G DP D Sbjct: 199 SFCGITGLKVTVGRVSTAGVLPLSTTLDTPGPMARSVEDVALLYNVLQGPDPLDPNTRGV 258 Query: 244 PAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPHTP 303 D L +RG+R+G G P++ AA A++++ GAE+ + LP Sbjct: 259 VPVDPLPGLERGVRGMRLGRMPAAEREGCAPEMLAAYDRALDLVDRLGAEIVDTRLPF-- 316 Query: 304 YALPVYYLIAPAEASANLARF-DGVRYGLRVPGESYFDE--LERTRGAGFGPEVRRRIML 360 RF D V V E+YF + A +VR RI+ Sbjct: 317 -------------------RFVDFVNAAAIVNAEAYFHNGAIAEDFAAPLDEDVRARILS 357 Query: 361 GTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAHTDDPLAM 420 G + Y R ++++ ++R + +A +D + PTT T A + A D + Sbjct: 358 GASVSARDYL-----RTRRLQQDMKRAFDRAMAGLDALLTPTTETAAIPLDA-VDQAV-- 409 Query: 421 YLEDVCTLPLNLAGLPGLVVPCGF-AEGLPIGLQLIGRAFDEESLLRVGDAYQRVTDWHT 479 + T N L L +PCGF AEGLP+ LQ+ R ++E + LR+G AYQ+ TDWH Sbjct: 410 -VPSRFTRFGNFLELCALALPCGFTAEGLPLSLQIACRGYEEATALRIGQAYQQATDWHG 468 Query: 480 RMP 482 R+P Sbjct: 469 RLP 471 Lambda K H 0.320 0.136 0.398 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: 561 Number of extensions: 30 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: 490 Length of database: 473 Length adjustment: 34 Effective length of query: 456 Effective length of database: 439 Effective search space: 200184 Effective search space used: 200184 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: 52 (24.6 bits)
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