Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_012976317.1 AZL_RS20170 AtzE family amidohydrolase
Query= curated2:Q67KJ2 (488 letters) >NCBI__GCF_000010725.1:WP_012976317.1 Length = 469 Score = 258 bits (660), Expect = 2e-73 Identities = 172/461 (37%), Positives = 240/461 (52%), Gaps = 38/461 (8%) Query: 14 GELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGDTELGPLAGVPI 73 G LSA + E+AL RIA++ P + AF V AD A +LDAR AG + GPLAGVP+ Sbjct: 20 GGLSATAVTEAALDRIARLNPVLNAFTDVTADRARREAAELDARIAAG-ADPGPLAGVPV 78 Query: 74 AVKDNICTSGMETTCASRILKGYV-SPFDATVVERLRAAGAMIIGKANMDEFAMGSSGES 132 AVK+ G+ T SRI + + DA ++ RL AAGA+++G NM E+A +GE+ Sbjct: 79 AVKNLFDIGGLPTRAGSRINRDRPPATADAVLLRRLTAAGAVLVGGLNMGEYAYDFTGEN 138 Query: 133 SAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAAFTGIVGLKPTY 192 + G RNP D R+ GGSSSG AA AAG APL+LG+DT GSIR P++F GI GLKPTY Sbjct: 139 AHDGACRNPHDPSRMAGGSSSGCGAATAAGLAPLSLGSDTNGSIRVPSSFCGIFGLKPTY 198 Query: 193 GYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGR-TPPALKFGGEP 251 G ++R+G F SLD +GP R V D+A ++V+ GP D AGR PAL Sbjct: 199 GRLTRHGSFPFCDSLDHLGPFARSVRDLALAYDVLQGPAEGDHACAGRPVEPALPALDAS 258 Query: 252 SLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLPSTEYALSAYYVIAV 311 L G+R+ V G P +A+A+ + T LP E +A Y+I Sbjct: 259 GLDGLRIAVAGGYFARGGQP----EAHDAVARAAQALGTDRVVELPGAELGRAAAYIITN 314 Query: 312 AEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLGTYVLSAGHYDAY 371 AE+S+ H +TR F + + R + G + + A+ Sbjct: 315 AESSA-------------------FHLERLRTRAGDFDPDTRDRFLAGALLPA-----AW 350 Query: 372 YRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKV------DDPVSMYLGDICT 425 Y +AQ+VR F D L+ P TP TA +G K + PV +LG + T Sbjct: 351 YVQAQRVRRWYHDRVMALFREVDVLLAPATPCTAPLVGRKTMVLDGREMPVRPHLG-LFT 409 Query: 426 IPVNLAGLPAVSVPCGFVDGLPVGMQLIGKPFADTQILQIA 466 P++ GLP +VP P+G+Q+I P+ + L++A Sbjct: 410 QPISCIGLPVCAVPMAPPGAPPIGIQVIAAPWREETCLRVA 450 Lambda K H 0.318 0.135 0.391 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: 690 Number of extensions: 39 Number of successful extensions: 7 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: 488 Length of database: 469 Length adjustment: 34 Effective length of query: 454 Effective length of database: 435 Effective search space: 197490 Effective search space used: 197490 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 (21.7 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