Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_086508848.1 BZY95_RS04860 amidase
Query= curated2:B8J405 (486 letters) >NCBI__GCF_002151265.1:WP_086508848.1 Length = 467 Score = 187 bits (474), Expect = 9e-52 Identities = 158/484 (32%), Positives = 229/484 (47%), Gaps = 62/484 (12%) Query: 13 AQALQKKELSAVDVTTACLDRITATEPHLAALLYVNAENALARATTLDS---EGPDAARP 69 A AL+ LSA ++ A + H A L E ALA A D+ +G D+ P Sbjct: 15 AAALRNGTLSASELAEAACAAYASRGKHDNAYLTWQGEAALAFARATDALIAQGGDSG-P 73 Query: 70 LWGVPVTLKDAFSTRGMPTTAGS-RML----EGYTPFYDAFAVQKLHEAGAVILGKTNLD 124 L G+PV++KD ++ G+PT AGS R L E P +A Q ++GKT+ Sbjct: 74 LMGIPVSIKDIYAVPGLPTYAGSSRRLPASWERPGPIVEALLAQL-----PSLMGKTHTV 128 Query: 125 EFAMGSSTENSAFKVTRNPWN--LNKVPGGSSGGSAASVTAGQCFASLGTDTGGSIRQPA 182 EFA G N+ + RNPW+ ++ PGGSS G+ S+ +G +LGTDT GS+R PA Sbjct: 129 EFAFGGLGTNAHWGAPRNPWDSQAHRTPGGSSSGAGVSLISGTAGLALGTDTAGSVRIPA 188 Query: 183 SFCGCVGLKPTYGRVSRYGVIAYGSSLDQVGPLTRSVEDCARVLTAIAGYDSRDNTCDPR 242 S G GLK T GR ++ ++LD G L R V+D A +D+ D PR Sbjct: 189 SMTGVAGLKTTAGRWPAQQIVPLSTTLDTPGLLARRVDDLA------YAFDALDANLSPR 242 Query: 243 PAEDYAATLSSRP-LKGARLGIPREFYGQGLSDEVRAACEAAIQAARNQDAELVEVSLPH 301 P + +S+ P L G+P F+ S + A + AI+ A +V + LP+ Sbjct: 243 P-----SPVSATPELADLTFGVPESFFWDDCSPGIAEAVQQAIRQLEAAGARVVTLELPN 297 Query: 302 TDAAIATYYIIAMAEASSNLARFDGVRFGHRSADIKNLDDLYVHSRTEGFGPEVKRRIML 361 TD A + +A A LA F A++ ++D P V RI Sbjct: 298 TDEAYELFQKGGLAAA--ELAAF-------LKAELPEMED--------ALDPNVAARIRA 340 Query: 362 GAYVLSSGYYDAYYRKAAQVRRLIRDELLAA----LGQCDALLAP---VSPVTARDLGGN 414 + + Y RR + DEL A +GQ DA+L P ++P T L Sbjct: 341 ADDMPAWEYVR---------RRSLLDELCTAATERMGQVDAVLTPTVAITPPTLESLEPE 391 Query: 415 TADPLQIYLMDAYTLSLNLAGLPGLSLPVGLGAKSGMPVGMQIIGKPFEETQVLALGHSL 474 A P T+ N GL GL+LPVG A +GMPVG+Q++ P++E ++LA+G ++ Sbjct: 392 GAYPKANMKALRNTVMANFMGLCGLTLPVGRDA-AGMPVGLQVLAGPWQEARLLAIGQAI 450 Query: 475 EQAL 478 E L Sbjct: 451 EAKL 454 Lambda K H 0.317 0.133 0.388 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: 519 Number of extensions: 30 Number of successful extensions: 6 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: 486 Length of database: 467 Length adjustment: 33 Effective length of query: 453 Effective length of database: 434 Effective search space: 196602 Effective search space used: 196602 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 10 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