Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012978377.1 AZL_RS31315 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_000010725.1:WP_012978377.1 Length = 498 Score = 220 bits (560), Expect = 1e-61 Identities = 164/471 (34%), Positives = 224/471 (47%), Gaps = 39/471 (8%) Query: 1 MTPLYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAAD 60 M + L++A+ R +A G +SS+EL +A L RI V P V A + +D GAR A AD Sbjct: 1 MPSVADLSLAEMRRRIADGSLSSVELLEACLARIDLVNPAVNAVVALDIDGARKAAEQAD 60 Query: 61 ARRAAGDA-SPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVIL 119 A GD PL GIP+ +KD T GLRTT S + N+ P D +VARL+AAGA+I Sbjct: 61 AAMRRGDGVGPLHGIPLLVKDTQDTAGLRTTYGSPLFANHVPAADQGSVARLRAAGAIIF 120 Query: 120 GKLNCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSI 179 GK N E+A G +T N T NP++ R GSSGGSA A+A G AP A G+DTGGS+ Sbjct: 121 GKTNTPEWAAGGNTRNPVHGATGNPFDPLRSSAGSSGGSAVALACGMAPIATGSDTGGSL 180 Query: 180 RQPAALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDAT 239 R PA GI G++P+YG V+ S+L GPMAR V D A++L V+A D D Sbjct: 181 RNPAGYAGIVGMRPSYGLVASERRAIGWSNLSTDGPMARNVADLALMLSVMASDDGRDPL 240 Query: 240 CTDYP-------APDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGA 292 P A + + D+ LRI ++ A ++ R + + A Sbjct: 241 AYSLPGETVRGRADRWFPVIPADLSRLRIAATEDFGFAPTAQEIRRVFRDRVRHIAPL-A 299 Query: 293 EVCEISLPHTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGP 352 C + P A + ++ + A AR R R GP Sbjct: 300 GACVEATPDCAGADDAFAVLRASVFLAMHAR------------------TFRERPDMLGP 341 Query: 353 EVRRRIMLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPT---TPTVAFK 409 VR I G GY Y RA +T I R +Q F D++ +PT +P + Sbjct: 342 NVRANIEEGL-----GYSLEDYTRAATTQTRIYRSFQSFFATHDLLISPTITVSPRPWSE 396 Query: 410 IGAHTDD--PLAMYLEDVC-TLPLNLAGLPGLVVPCGFAE-GLPIGLQLIG 456 + D P Y + + LAG P L +P G E G+P GLQ++G Sbjct: 397 LYPREIDGRPTRSYFHWLALAYGVTLAGHPALSLPVGLDESGMPFGLQIVG 447 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: 601 Number of extensions: 35 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: 1 Length of query: 490 Length of database: 498 Length adjustment: 34 Effective length of query: 456 Effective length of database: 464 Effective search space: 211584 Effective search space used: 211584 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