Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_051305549.1 G494_RS22650 amidase
Query= curated2:A6TTJ8 (491 letters) >NCBI__GCF_000429965.1:WP_051305549.1 Length = 463 Score = 218 bits (555), Expect = 4e-61 Identities = 161/483 (33%), Positives = 237/483 (49%), Gaps = 38/483 (7%) Query: 5 EMTIMDIRKGYVQKQFTVKDVVQGYIDRIKELDGKINAFITLCEESALMEAAVLDEKLSR 64 + ++ + Q + ++VV+ Y+ +I+ ++ K+NA + L ESAL +A D+ L++ Sbjct: 7 QQSLSSLASAIQTNQVSSREVVESYLRQIRRVNPKLNAVVRLSAESALAQATRADQALTK 66 Query: 65 GEEIGLLGGIPVAIKDNMCTQGIKTSCASEMLADFIPPYDATIVKKLRAAGAIIIGKTNM 124 G +G L GIP+ IKD+ T GI ++ + +DFIP DAT+V +LRAAGAI++GKTN Sbjct: 67 GTLLGPLHGIPMTIKDSFDTAGIVSTGGTLGRSDFIPTRDATVVSRLRAAGAILLGKTNT 126 Query: 125 DEFAMGSSTENSAFKVTKNPWDLTKVPGGSSGGSAAALAAGFAPLTIGSDTGGSIRQPAA 184 EF + +N + T NP+DL + GGSSGG+AA +AAG +P IGSD GGS+R PA Sbjct: 127 SEFTLSYDADNLLYGRTSNPYDLQRSSGGSSGGAAAIVAAGGSPFDIGSDYGGSLRYPAH 186 Query: 185 FCGTVGLKPTYGLVSRFG-LIAFASSLD---QIGPFTKTVKDCALSLQVMQGNDPLDSTS 240 CG +KPT G V R G ++ F LD Q+GP + V+D L L ++ G D +D + Sbjct: 187 CCGVCTIKPTSGRVPRTGHILPFGGMLDSFQQVGPIARRVEDLQLLLPLICGPDNIDPSI 246 Query: 241 IQQEPMDDYVKDLDKGVKGLKVGIPKEFFQEGLNIEISDSIKEAIKVLEQLGAVVEEFSL 300 + + +L L+V + + E + ++ A +LEQ VVEE Sbjct: 247 VPMPLAEPGSIELG----SLRVSYHTDNGILPASPETREVVRRAAAILEQERLVVEE--- 299 Query: 301 PVTDSGLSAYYIISSAEASSNLARYDGVRYGHRAAVYEGIEEMMLNSRSEGFGKEVKRRI 360 +GL Y E L DG R G EE + G K Sbjct: 300 -ARPAGLEQSY-----ELGLGLWSADGGAMIERLLTEHGTEEHTIPWL--GLAKP----- 346 Query: 361 MLGTYVLSSGYYDAYYKKAMDFRKKTRNVFKKAFESYDVILTPTSPVLPFTIGEKTGDPL 420 L +G DA + +R ++ F+ YD+IL P + G D Sbjct: 347 ------LDAGQLDALLVRWYQYRSSMLSI----FQDYDLILCPVNAHPALAHGAIGAD-- 394 Query: 421 EMYLADIYTVNVNIAGVPAISIPCGFSKEKLPIGLQLIGDHYSEKKLLQAAYGLEQELGI 480 A YT N+ G PA+ + G S LPIGLQ++ + E L A LEQ LG Sbjct: 395 --LRAFSYTSAYNLTGWPAVVLRGGTSATGLPIGLQIVAAPWREDLALALAAFLEQALGT 452 Query: 481 FKE 483 F + Sbjct: 453 FPQ 455 Lambda K H 0.317 0.136 0.382 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: 495 Number of extensions: 24 Number of successful extensions: 3 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: 491 Length of database: 463 Length adjustment: 33 Effective length of query: 458 Effective length of database: 430 Effective search space: 196940 Effective search space used: 196940 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 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