Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate HSERO_RS12060 HSERO_RS12060 indole acetamide hydrolase
Query= curated2:A7NKM0 (490 letters) >FitnessBrowser__HerbieS:HSERO_RS12060 Length = 468 Score = 223 bits (568), Expect = 1e-62 Identities = 167/491 (34%), Positives = 242/491 (49%), Gaps = 41/491 (8%) Query: 4 LYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADARR 63 L +T+ + R+ L+ S LE DAL+ A + + +L D R+QAR D + Sbjct: 3 LVDMTLIEVRQGLSDRRFSCLEYVDALIAETEA-QWDLNCYLQRDPEQLRSQARMLDEQ- 60 Query: 64 AAGDASPLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGKLN 123 G PL GIP+ IKD I G+ +T + L N P AT V L AGA+ GK N Sbjct: 61 --GGHGPLSGIPIAIKDNIDVAGIASTAGTAALRNNVPQRHATVVEYLFGAGALHAGKAN 118 Query: 124 CDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQPA 183 E A G + N F RNP++ E + GGSSGG A +AA APAA+GTDTGGS+R PA Sbjct: 119 MHELAFGITNNNGVFGPCRNPYDAELIAGGSSGGCGALLAARLAPAAVGTDTGGSVRIPA 178 Query: 184 ALCGITGLKPTYGRVSRYGLVAFASSLDQIGPMARTVRDCAIVLRVIAGADPFDATCTDY 243 ALCG+ GL+PT R S++G+V + + D GPMAR+V D A++ +++AG Sbjct: 179 ALCGVVGLRPTSRRYSQHGVVPISHTRDTPGPMARSVADVALLDQIMAG----------- 227 Query: 244 PAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAEVCEISLPH-T 302 + D L LR+GV R G++ +VEA A+ LRE G E+ ++ LP Sbjct: 228 -SRDSAPLLALPPSQLRLGVLRNPSWQGLEEEVEANANAALMQLREAGVELVDVDLPTLA 286 Query: 303 PYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPEVRRRIMLGT 362 P + + I E +L + + D ++R P+V R I Sbjct: 287 PLSHAAGFAIVLHEFLIDLPAY--------LQASDARDVIKRVLAEVGSPDVARIIQA-- 336 Query: 363 YALSAGYYDAYYKRAQQVRTLIRRDYQQAF--EQVDVIAAPTTPTVAFKIGAHTDDPLAM 420 L + Y+ A + R ++ Y+ F + VD + PTT A +G DD +A+ Sbjct: 337 -TLDQPVPEHAYRLALEQRRTMQALYRDCFRSQGVDALIFPTTALTARPLG--EDDTVAL 393 Query: 421 YLEDVCTLP--------LNLAGLPGLVVPCGFAE-GLPIGLQLIGRAFDEESLLRVGDAY 471 E V T P ++AGLP + +P G +E GLP+GL+L G + LL+V + Sbjct: 394 RGERVPTFPAFARNADGASIAGLPSISIPVGLSEYGLPVGLELDGPEGSDRRLLQVAASL 453 Query: 472 QRVTDWHTRMP 482 + V R P Sbjct: 454 ETVLGRGPRPP 464 Lambda K H 0.320 0.136 0.398 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: 488 Number of extensions: 24 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: 490 Length of database: 468 Length adjustment: 34 Effective length of query: 456 Effective length of database: 434 Effective search space: 197904 Effective search space used: 197904 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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