Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate RR42_RS36060 RR42_RS36060 amidase
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__Cup4G11:RR42_RS36060 Length = 468 Score = 231 bits (590), Expect = 3e-65 Identities = 163/490 (33%), Positives = 239/490 (48%), Gaps = 37/490 (7%) Query: 2 LSAARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAG 61 L A + R EL E+ ++ ++RI ++ PA+ A +T D A D G Sbjct: 7 LGAVEMARAIRTRELGVREVVDAHIARILRINPAINAIVTTTFDEAQAAADAADTALARG 66 Query: 62 DTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANM 121 GPL G+P+A KD+ ++G+ TT S + + +V D+ VV R RAAGA+++GK N+ Sbjct: 67 AVP-GPLFGLPVAHKDSFLSAGVRTTFGSAVYRDFVPAQDSAVVARQRAAGAIMLGKTNL 125 Query: 122 DEFAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAA 181 EF GS ++ FG TRNP+ + GGSS GSAAA+AAG LA G+D GGS+R PA+ Sbjct: 126 PEFGAGSHTFNAVFGATRNPYRKDVSAGGSSGGSAAALAAGMVALADGSDMGGSLRNPAS 185 Query: 182 FTGIVGLKPTYGYVSRYGVVAFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDATNAGRT 241 F +VGL+ + G V ++L GPMGR V DVA +F V+AG D D Sbjct: 186 FCNVVGLRASIGRVPMTPASHAFNTLTVGGPMGRSVADVALMFSVLAGDDPADP--LAIA 243 Query: 242 PPALKFGGEPSL--SGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECSLPST 299 A F P + G+R+ V L G +P V ++E I Q + LG TV+E P Sbjct: 244 ADASDFATLPRIDGKGLRVAVSPTLGGLPFEPAVSRMLQEGIRQCQALGCTVDEAE-PDF 302 Query: 300 EYALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRGEGFGTEVKRRIMLG 359 A A+ V+ ++N Y AA+A GE V+ I LG Sbjct: 303 SGADHAFEVLRALAFAAN----------YGAARA---------KHGEQMKETVRWNIDLG 343 Query: 360 TYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVDD----- 414 A A + + + + RYD L+ P + T + + + Sbjct: 344 -----LAQDGAAMAEAARAHSRMFARMQALLTRYDFLIAPVSQVTPFAVETEYPQHIEGV 398 Query: 415 PVSMYLGDI-CTIPVNLAGLPAVSVPCGFV-DGLPVGMQLIGKPFADTQILQIAWAYQKV 472 P+ Y+G + + + G PA+SVPCGF DGLPVG+Q++GK + +L A +++ Sbjct: 399 PMPSYIGWMRSCYRITITGHPAISVPCGFTDDGLPVGLQIVGKYRGERALLAFAQMFEQA 458 Query: 473 TKHHEARPAL 482 RPAL Sbjct: 459 NAAGRIRPAL 468 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: 595 Number of extensions: 36 Number of successful extensions: 4 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: 468 Length adjustment: 34 Effective length of query: 454 Effective length of database: 434 Effective search space: 197036 Effective search space used: 197036 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