Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate RR42_RS00215 RR42_RS00215 branched-chain amino acid ABC transporter ATP-binding protein
Query= curated2:Q7UT33 (499 letters) >FitnessBrowser__Cup4G11:RR42_RS00215 Length = 429 Score = 190 bits (483), Expect = 7e-53 Identities = 154/479 (32%), Positives = 221/479 (46%), Gaps = 65/479 (13%) Query: 5 ASEILKQLDSGEVTAVEVIAQSLAAIRASQPTINAFTHVAEETAMQAAEAVDADRKAGKT 64 A E+ ++ E++ ++ +A I A++ I A+ H A+Q A +DA G Sbjct: 9 ARELAARMARRELSVQALVRAYIARIDAAEAGILAWQHFDGAQALQQARQLDA----GPA 64 Query: 65 LGPLAGLPVAIKDVLCTSDMPTTCSSKMLEGFVPPYDATVVARLKSAGAIVVGKTNMDEF 124 LG L GLP+ +KD++ T+DMPTT S + G P DA VA ++AGA+V+GKT EF Sbjct: 65 LGALHGLPIGVKDLMDTADMPTTYGSPIYAGHRPVMDAACVAMARAAGAVVMGKTVTTEF 124 Query: 125 AMGASTETSAMGVTGNPW---DTTKTPGGSSGGAAAAVAAGAVPLSLGTDTGGSIRQPAA 181 A T G T NP D +TPGGSS G+AAAVAAG VP++ GT T GSI +PAA Sbjct: 125 A------TFQPGPTRNPRAPADAPRTPGGSSSGSAAAVAAGMVPIAFGTQTAGSIIRPAA 178 Query: 182 FCGITGLKPTYGRVSRYGLVAFASSLDQAGPMGWSVDDVAIGLQAMAGYDPRDSTSVNAE 241 +CG+ G KPT+G + G+ + + SLD G + VDD A + AM A Sbjct: 179 YCGVVGYKPTFGTLPSAGIKSLSPSLDTVGVLARCVDDAAFFIGAM------------AR 226 Query: 242 VPDFTPAMAAEDVRGMRIGVLREGLDQDGISPAVRDALATAESVFREQGAEIVEVELPHS 301 +P TP A + R +R+G+ R + R AL TA +GA + ++ LP Sbjct: 227 LP-LTPPQAGQATR-LRVGICRTP-HWERAGDDSRRALDTAARWLEGRGAVLSDLILP-- 281 Query: 302 KYWVPTYYVIAPCEASSNLSRFDGAHYGYRVADAEIAAADSGPLEAMYSLSRAGGFGSEV 361 ++FD A +I A ++ A +R GF S Sbjct: 282 -------------------AQFD----ELTQAQIDIMAYEAAAAFAPEMRARPDGFSSGF 318 Query: 362 KRRIMVGTYALSEGYYDAYYNQALKVRRLIRNDYDAAFQQVDLMLGPVTPSPAFALNEKT 421 + G G + + A + R + F VD++L P P A A T Sbjct: 319 AALLAAG-----RGIDGSRFFAAQALAGSARRAFGQMFDSVDIVLAPSAPGEAPAGLGAT 373 Query: 422 DDPIAMYLCDLFTVGANLAGVPAISLPGGFDAVGLPVGVQLQAPVMEETRLLRAGNVFQ 480 DP +F L G P + +P A G+PVGV L P + R+L A + Sbjct: 374 GDP-------MFNRMWTLLGNPCVHVPTSTGAHGMPVGVTLIGPCRGDARVLAAAQALE 425 Lambda K H 0.316 0.132 0.381 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: 556 Number of extensions: 38 Number of successful extensions: 5 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: 499 Length of database: 429 Length adjustment: 33 Effective length of query: 466 Effective length of database: 396 Effective search space: 184536 Effective search space used: 184536 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: 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