Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_011423609.1 RHE_RS01105 amidase
Query= curated2:B8J405 (486 letters) >NCBI__GCF_000092045.1:WP_011423609.1 Length = 463 Score = 176 bits (446), Expect = 2e-48 Identities = 145/490 (29%), Positives = 227/490 (46%), Gaps = 56/490 (11%) Query: 7 LSLTAVAQALQKKELSAVDVTTACLDRITATEPHLAALLYVNAENAL--ARATTLDSEGP 64 L++ + + K LS ++ + D + A EP ++AL + E A A+A+T Sbjct: 6 LTIRELRRRFADKSLSPLEYWLSLEDHVAAWEPSISALYLYDPEAARVQAKASTERWAKG 65 Query: 65 DAARPLWGVPVTLKDAFSTRGMPTTAGSRMLEGYTPFYDAFAVQKLHEAGAVILGKTNLD 124 L G+P TLK+ +T G P G+R +E DA A +L E GAVI KT Sbjct: 66 RTLGTLDGIPATLKELIATEGQPVPLGTRAVELKPAEADAPAAARLREDGAVIFAKTTCP 125 Query: 125 EFAMGSSTENSAFKVTRNPWNLNKVPGGSSGGSAASVTAGQCFASLGTDTGGSIRQPASF 184 ++ M SS +S ++RNPWN+ + PGGSS G+AA+ AG +GTD GGS+R PA + Sbjct: 126 DYGMLSSGLSSFHPLSRNPWNIAQNPGGSSAGAAAAAAAGYGPLHIGTDIGGSVRLPAGW 185 Query: 185 CGCVGLKPTYGRVSRYGVIAYGSSLDQVGPLTRSVEDCARVLTAIAGYDSRDNTCDPRPA 244 G G KP++GR+ G L GP+TR+VED A + ++ D RD T P Sbjct: 186 TGIFGFKPSHGRIPA-DPYYVGRCL---GPMTRTVEDAAFSMATLSRPDWRDGTSLPPND 241 Query: 245 EDYAATLSSRPLKGARLGIPREF-YGQGLSDEVRAACEAAIQAARNQDAELVEVSLPHTD 303 D+ + + G ++G+ + G + DE+R A E+A + A +V V T Sbjct: 242 FDWMDFVVD--ISGMKIGLMLDAGCGFAVDDEIRVAVESAAKRFEKAGATIVSVQPVLTR 299 Query: 304 AAIATYYIIAMAEASSNLARFDGVR----------FGHRSADIKNLDDLYVHSRTEGFGP 353 A + A S++A + R + ADI +D GF Sbjct: 300 AMLDGLDTFWRARLWSDIAGLNEERRDSILPYIRDWAKAGADISGVD------AVRGFNQ 353 Query: 354 EVKRRIMLGAYVLSSGYYDAYYRKAAQVRRLIRDELLAALGQCDALLAPVSPVTA--RDL 411 ++ R G RL + DALL+P +P+ + + Sbjct: 354 TIEMRRSCG--------------------RLFT--------RVDALLSPTNPIISYPAEW 385 Query: 412 GGNTADPLQIYLMDAYTLSLNLAGLPGLSLPVGLGAKSGMPVGMQIIGKPFEETQVLALG 471 T DP + + A+T+ N++ P S+ G ++SGMP+G+QI+G F++ +VL L Sbjct: 386 ASPTNDPTRPFEHIAFTVPWNMSEQPAASINCGF-SRSGMPIGLQIVGPRFDDMRVLRLS 444 Query: 472 HSLEQALPGI 481 + E G+ Sbjct: 445 KAFEDWTGGV 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: 492 Number of extensions: 15 Number of successful extensions: 3 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: 486 Length of database: 463 Length adjustment: 33 Effective length of query: 453 Effective length of database: 430 Effective search space: 194790 Effective search space used: 194790 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