Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_068172310.1 HTA01S_RS13400 amidase
Query= curated2:B8HY89 (482 letters) >NCBI__GCF_001592305.1:WP_068172310.1 Length = 469 Score = 265 bits (677), Expect = 3e-75 Identities = 169/481 (35%), Positives = 254/481 (52%), Gaps = 28/481 (5%) Query: 2 ASIRELHQQLVSKERSAKEITQDALEKIQQLEPKVHAFLTLTAEQALAQAERVDQQIATG 61 ASI E+ L + E ++ + + L++IQ+L+ ++HAF+ + AE+A A +D G Sbjct: 11 ASIEEVVSALDAGELTSVSLVEQQLDRIQRLDHQLHAFVDVYAEEAREAAHAMDGLRRAG 70 Query: 62 TEIGLLAGIPIAIKDNLCTKGIPTTCGSKILQGFIPPYESTVTSRLAAAGAVMVGKTNLD 121 +G L G+ +A+KD G P T GS L I +TV RL +AGA+++GKT+ Sbjct: 71 VRLGPLHGVTVAVKDLFHIGGKPITGGSVALPARISTTTATVVERLRSAGAIVIGKTHTV 130 Query: 122 EFAMGSSTENSAYQLTANPWDLQ--RVPGGSSGGSAAAVAAGETLIALGSDTGGSIRQPA 179 E+A G N NPWDLQ RVPGGSS GSA AVAAG A+G+DTGGS+R PA Sbjct: 131 EYAFGGWGTNEVMGTPWNPWDLQTHRVPGGSSSGSAVAVAAGLACAAIGTDTGGSVRIPA 190 Query: 180 SFCGVVGLKPTYGLVSRYGLVAYASSLDQIGPFATNVEDAALLLGAIAGHDPQDSTSLNV 239 CG+VGLK T+GL+SR+GL+ + D +GP A +V D ALLL +AG DP+D S + Sbjct: 191 GLCGLVGLKTTHGLISRHGLIELCPTHDTVGPLARSVRDCALLLDVMAGADPRDPVSQDA 250 Query: 240 PIPDYTQFLIPDLKGKKIGIIQETYGEGLDPQVEQVTHKAIQQLEELGAEVREISCPRFR 299 P+ + +G ++ ++ EG++ V +A+ L+ LG ++ E P Sbjct: 251 PVRRVIDGVNAMPRGARLWVLPVQEREGVEAAVLAAYDEALAMLKGLGMQLVEKPLP--- 307 Query: 300 YGLPTYYIIAPSEASANLARYDGVKYGFRSPDPENLLSMYTRTRAEGFGPEVKRRIMIGT 359 ++ A+ R G D NL +++ R+ F ++RR+++G Sbjct: 308 ------------QSCADSMRIAGQLMSAEGYD--NLGALFERSDLR-FDANIRRRVLLGR 352 Query: 360 YALSAGYYDAYYLKAQKVRTLIKQDFEAAFEQVDVLVCPTAPTTAFAAGAKTADPLSMYL 419 + YL+ + R L + D AA + ++ V PT +A D L+ L Sbjct: 353 DTAA-----GEYLRLLRARDLARNDMLAAMDGIEACVFPTNAISAIPVA--DVDELATPL 405 Query: 420 SDLMTIPVNLAGLPGLSLPCGFDQQGLPIGLQLIGNVLREDLVFQVAYAYEQATPWHDRH 479 S VNL L L++P G +G+PI +Q IG E LVF++ +A+EQATPWH Sbjct: 406 SRFGRF-VNLMNLCSLAVPAGLSPEGMPISIQFIGRPWDEPLVFRLGHAFEQATPWHGLR 464 Query: 480 P 480 P Sbjct: 465 P 465 Lambda K H 0.317 0.134 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: 530 Number of extensions: 18 Number of successful extensions: 3 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: 482 Length of database: 469 Length adjustment: 33 Effective length of query: 449 Effective length of database: 436 Effective search space: 195764 Effective search space used: 195764 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 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