Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate GFF1174 PGA1_c11890 putative indoleacetamide hydrolase
Query= curated2:Q67KJ2 (488 letters) >FitnessBrowser__Phaeo:GFF1174 Length = 480 Score = 180 bits (457), Expect = 8e-50 Identities = 144/468 (30%), Positives = 213/468 (45%), Gaps = 43/468 (9%) Query: 2 LSAARLNRLFLAGELSAVEIAESALSRIAQVEPAVGAFITVAADHVIERAKKLDARRKAG 61 LSA L+R AG+L+A ++L+R+ V P + A + + + RA++LD R +G Sbjct: 9 LSATELSRRTTAGDLTAEAAVAASLTRMTAVNPDLNAVVEDLSSEALGRAQQLDKARASG 68 Query: 62 DTELGPLAGVPIAVKDNICTSGMETTCASRILKGYVSPFDATVVERLRAAGAMIIGKANM 121 GPL GVP+ +K N+ +G T+ LK ++ DA VV+ L+ AGA++IG+ N Sbjct: 69 -APCGPLHGVPVTIKINVDQAGHATSNGVSALKDLIAADDAPVVKNLQDAGAVVIGRTNT 127 Query: 122 DEFAMGSSGESSAFGVTRNPWDLERVPGGSSSGSAAAVAAGEAPLALGTDTGGSIRQPAA 181 EF+ + ++ G T NPW PGGSS G+ AAV AG LA G D GGS+R PAA Sbjct: 128 PEFSFRADTDNPLHGRTHNPWGRHISPGGSSGGAGAAVMAGIGALAHGNDIGGSLRFPAA 187 Query: 182 FTGIVGLKPTYGYVSRYGVV------AFASSLDQVGPMGRDVEDVARLFEVIAGPDRRDA 235 G V +KP G V + A ++ G + R +D+ + PD RD Sbjct: 188 ANGAVTVKPGLGRVPAWNPSQSAERGILAQNMSVQGLLTRTAQDLHLSMPSLIAPDPRDP 247 Query: 236 TNAGRTPPALKFGGEPSLSGVRLGVPKELLGPGIDPGVKARVEEAIAQLEELGATVEECS 295 + P G P +R+ KE G + P V A +E+A A L + G VEE Sbjct: 248 FHV----PLPWHGASPD-GPIRVAFSKETYGYDLHPEVDAALEDARAALSDAGYLVEETV 302 Query: 296 LPSTEYALSAYYVIAVAEASSNLARFDGVRYGYRAAQAGGLHEMYSKTRG--EGFGTEVK 353 LP FD R GYRA + E+Y+ +G + G++ Sbjct: 303 LPDV---------------------FDAGRTGYRAL----MGEVYALMKGDVDAAGSQTV 337 Query: 354 RRIMLGTYVLSAGHYDAYYRRAQQVRTLVVRDFERAFERYDALVTPTTPFTAWKIGEKVD 413 R I + + RT RD+ +RY ++TP P ++ + Sbjct: 338 RDIFAVYFEEFPPFAGVELLQMMAKRTQYARDWSLFMQRYPLVLTPFLPQPFFRPDRDTE 397 Query: 414 DPVSMY--LG-DICTIPVNLAGLPAVSVPCGFVDGLPVGMQLIGKPFA 458 ++ LG + + +N GLPA SVP + LP G Q I A Sbjct: 398 GAAGVHEVLGCAVYSYAMNFLGLPAASVPSRLAE-LPSGPQPINVQIA 444 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: 524 Number of extensions: 32 Number of successful extensions: 5 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: 480 Length adjustment: 34 Effective length of query: 454 Effective length of database: 446 Effective search space: 202484 Effective search space used: 202484 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: 52 (24.6 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