Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate BWI76_RS13990 BWI76_RS13990 allophanate hydrolase
Query= curated2:C1F857 (476 letters) >FitnessBrowser__Koxy:BWI76_RS13990 Length = 598 Score = 162 bits (409), Expect = 4e-44 Identities = 148/471 (31%), Positives = 212/471 (45%), Gaps = 43/471 (9%) Query: 14 RTGEVRAEAALQECLGAIDAHNGEVNAYLS-LDRDGAGARARHIDALSREERAKLPMGGV 72 R G+ L E A N E ++ L + ++ LS E LP+ GV Sbjct: 18 RNGKTTPRRLLAEVRQRAQALNPEFRLFIHILSEEEQEPLLAALEGLSPTE---LPLYGV 74 Query: 73 PFGIKDVLTVEGMPATASSKILEGYRPPYTATAVQRLIDAGAVLVGKLNCDEFAMGSSNE 132 PF IKD + + + TA+ YR +AT V +LI GAV VGK N D+FA G + Sbjct: 75 PFAIKDNIDLAEIITTAACPAF-AYRAEQSATIVAQLIALGAVPVGKTNLDQFATGLNGT 133 Query: 133 NSAYGPVKNPRALDRVPGGSSGGSAAAVAANMAVATLGTDTGGSIRQPASFCGVVGVLPT 192 S YG +N D GGSS GSA AVA +A +LGTDT GS R PA +VG+ T Sbjct: 134 RSPYGACRNGYLADYPSGGSSAGSALAVALGVASFSLGTDTAGSGRVPAGLNNLVGLKAT 193 Query: 193 YGRVSRYGLIAFASSLDRVGPFAHTVRDAAEVLGVIAGHDPMDATSSSVPVPDYTEKLDA 252 G +S G++ +LD V F+ T +A+++L ++A +DP+DA S P + + Sbjct: 194 KGLISTAGVVPACRTLDCVTFFSATADEASQLLALVAQYDPLDAWSRHNPQWNSRQAFGR 253 Query: 253 GVKGLRLGVPAEYFAEGLDPEVKRAVEGTIEQLRAAGAEVKPISLPHTPYAIPTYYVIAT 312 G R GVP E G +R ++L A G + + P+ Sbjct: 254 PAAGFRFGVPRELNFLGCSAS-ERLFTQARQRLTALGGVA--VEIEFAPFL--------- 301 Query: 313 AEASANLARFDG----VRYGLRAPEANTLAAMYRQTRDLGFGAEVKRRILLGTYVLSA-G 367 A+A L +DG RY + P M RQ + V R +L A Sbjct: 302 --AAARLL-YDGPWVAERYAVVGP------LMARQPEAV---LPVIREVLAKAPDTDATA 349 Query: 368 YYDAYYKKAQQVRRLLAQDFLRAFEEVDAIVTPTAPTPAFKLGEKSDDPLSMYLADI--Y 425 + A Y+ Q R A E +D ++TPT P P L E +P++ AD+ Y Sbjct: 350 TFKAIYQLQQYKARCDA-----ILETLDCVLTPTYPRPV-TLDELQAEPIARN-ADLGYY 402 Query: 426 TVTANLAGICGASVPCGTSREGLPIGIQILGRHFDEATVLRVGQAVESLQK 476 T NL SVPCG +GLP G+ + GR F + +L + A + ++ Sbjct: 403 TNFMNLLDYAAVSVPCGFMPDGLPSGVTLFGRAFTDQYLLSLADAFQRAER 453 Lambda K H 0.317 0.134 0.385 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: 734 Number of extensions: 39 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 476 Length of database: 598 Length adjustment: 35 Effective length of query: 441 Effective length of database: 563 Effective search space: 248283 Effective search space used: 248283 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: 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