Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate BPHYT_RS00720 BPHYT_RS00720 amidase
Query= curated2:A6TTJ8 (491 letters) >FitnessBrowser__BFirm:BPHYT_RS00720 Length = 475 Score = 204 bits (518), Expect = 7e-57 Identities = 154/470 (32%), Positives = 226/470 (48%), Gaps = 28/470 (5%) Query: 14 GYVQKQFTVKDVVQGYIDRIKELDGKINAFITLCEESALMEAAVLDEKLSRGEEIGLLGG 73 G+ Q + +V+ +DRI +LD +NAF L EE A+ A+ + + RGE G L G Sbjct: 15 GFRQCTLSPVEVMCEVLDRITKLDPVVNAFCALDEEEAMSAASEAERRWMRGEPCGPLDG 74 Query: 74 IPVAIKDNMCTQGIKTSCASEMLADFIPPYDATIVKKLRAAGAIIIGKTNMDEFAMGSST 133 +PV++KD + G+ T S + DA V +LR AGAI GKT EF T Sbjct: 75 VPVSVKDLVAVAGLPTRQGSWTASPDRESVDAPAVARLRRAGAIPFGKTTTSEFGNKIVT 134 Query: 134 ENSAFKVTKNPWDLTKVPGGSSGGSAAALAAGFAPLTIGSDTGGSIRQPAAFCGTVGLKP 193 + T+NPWD PGGSSGGSA A+A G PL++ +D GGSIR PA + G VG KP Sbjct: 135 DCPMTGATRNPWDTRLSPGGSSGGSAVAVALGLGPLSLATDGGGSIRIPACWSGVVGFKP 194 Query: 194 TYGLVSRFGLIAFASSLDQIGPFTKTVKDCALSLQVMQGNDPLDSTSIQQEP--MDDYVK 251 T+ LV G A ++L +GP T+TV+D AL L M G + ++ Y Sbjct: 195 TFALVPA-GSAASWTALSTLGPITRTVRDAALMLDAMTGTNTCANSDGPPGTGRTSAYSA 253 Query: 252 DLDKGVKGLKVGIPKEFFQEGLNIEISDSIKEAIKVLEQLGAVVEEFSLPVTDSGLSAYY 311 LD GV GL++ + +I++ + A+ LGA V +P + + YY Sbjct: 254 GLDDGVAGLRIAWCAAPAGVSVAPDIAECVGRAVDAFGTLGATV----IPTDVAPIVDYY 309 Query: 312 IISSAEASSNLARYDGVRYGHRAAVYEGIEEMMLNSRSEGFGKEVKRRIMLGTYVLSSGY 371 + + ++ V + R E + +L+ + RI T+V Sbjct: 310 ----GDGRIHSVQW-SVFFAQRVRHMEAADRTLLDPDLTALA-DAGARIDTATFV----- 358 Query: 372 YDAYYKKAMDFRKKTRNVFKKAFESYDVILTPTSPVLPFTIGEKTGDPLEMYLADIYTVN 431 A+ R + F+ YD+++TPT P + G + A + T Sbjct: 359 ------DALLARHALGASMETFFKHYDLLVTPTFHCGPPPVPSLPG---HLRNAPLLTAW 409 Query: 432 VNIAGVPAISIPCGFSKEKLPIGLQLIGDHYSEKKLLQAAYGLEQELGIF 481 N AGVPAIS+PCGF+ + +P GLQ+IG S+ +L+AA E G F Sbjct: 410 CNQAGVPAISVPCGFAGD-MPTGLQIIGRRGSDALVLRAARAYELARGDF 458 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: 493 Number of extensions: 20 Number of successful extensions: 4 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: 491 Length of database: 475 Length adjustment: 34 Effective length of query: 457 Effective length of database: 441 Effective search space: 201537 Effective search space used: 201537 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: 52 (24.6 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