Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate RR42_RS26835 RR42_RS26835 amidase
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__Cup4G11:RR42_RS26835 Length = 460 Score = 211 bits (536), Expect = 6e-59 Identities = 157/471 (33%), Positives = 235/471 (49%), Gaps = 44/471 (9%) Query: 3 SAARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAGD 62 S A + +G LSA ++ ++L+R AQV ++ + A + A D R AG Sbjct: 7 SVAGIAAQLRSGSLSAQDVVRASLARAAQVA-SLNCVSRLLAREAVVGAGACDTARLAGK 65 Query: 63 TELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPF--DATVVERLRAAGAMIIGKAN 120 L PLAGVP VK+ + G T A + P A VV+ L AAGA+ + Sbjct: 66 APL-PLAGVPFVVKNLLDVEG-HATLAGAHARANEPPATRSAAVVQALMAAGAIPVALTQ 123 Query: 121 MDEFAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPA 180 MDE+A G++GE+ G RNP D R+ GGSS+G+AAA+AAG AP+ +G+DT GSIR PA Sbjct: 124 MDEYACGATGENVIGGPVRNPLDPARIAGGSSAGTAAAIAAGIAPIGIGSDTNGSIRAPA 183 Query: 181 AFTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGR 240 +F GI GL+PT G +S G +A SLD VGPM D +A + + GP G Sbjct: 184 SFCGIWGLRPTTGRMSAQGCFPYAESLDAVGPMASDAAGLALAYRAMLGPG--SGPRPGE 241 Query: 241 TPPALKFGGEPSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLPSTE 300 PA S++G+R+G+ L G + ++A+ ++ V + LP + Sbjct: 242 PAPA----AGVSMAGLRVGI----LQAGFGDFAQDEAQDAVLRVASAFDAVRKIDLPEAD 293 Query: 301 YALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLGT 360 A A +I+ E N V+ G+ R G+ V++R++ G Sbjct: 294 LARDAASIISAFEVGRN-----HVQRGF-------------AERHPGYSAFVRQRMLAGL 335 Query: 361 YVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIG-EKVDDPVSMY 419 + + +Y+ A+ + + E F+ D L+ TTP+ A IG E++ Y Sbjct: 336 SI-----PEGWYQLAKAYQAAWRQKLEALFDEVDLLLACTTPYAAPLIGAEQIAGGKRAY 390 Query: 420 L----GDICTIPVNLAGLPAVSVPCGFVDGLPVGMQLIGKPFADTQILQIA 466 + T PV+LAGLP V+ PC V GLP+G+QLI P+ +T+ L+ A Sbjct: 391 VPRADAGHLTRPVSLAGLPVVAAPCA-VAGLPLGVQLIAPPWQETRCLEAA 440 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: 581 Number of extensions: 37 Number of successful extensions: 5 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: 460 Length adjustment: 33 Effective length of query: 455 Effective length of database: 427 Effective search space: 194285 Effective search space used: 194285 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 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