Align Glutamyl-tRNA(Gln) amidotransferase subunit A; Glu-ADT subunit A; EC 6.3.5.7 (uncharacterized)
to candidate WP_338063076.1 ABB28_RS15960 amidase
Query= curated2:A7NKM0 (490 letters) >NCBI__GCF_001431535.1:WP_338063076.1 Length = 498 Score = 236 bits (602), Expect = 1e-66 Identities = 180/495 (36%), Positives = 238/495 (48%), Gaps = 35/495 (7%) Query: 3 PLYQLTVAQAREMLARGEISSLELTDALLTRIAAVEPKVRAFLVVDAAGARAQARAADAR 62 P + L+ A +L RGE+S++ELT + L RIA V P V A VD A A A ADA Sbjct: 26 PAWALSATDASALLRRGELSAVELTRSCLGRIAVVNPVVNALNFVDEAAAIRAAEQADAA 85 Query: 63 RAAGDAS-PLLGIPMGIKDVISTQGLRTTCASKMLENYTPVYDATAVARLKAAGAVILGK 121 A G S PL GIP+ IKD +G T L++ DA VARL+AAGA++LG+ Sbjct: 86 LARGAVSAPLHGIPVAIKDNTDVRGQPMTNGIVALKDNIASADAPQVARLRAAGAIVLGR 145 Query: 122 LNCDEFAMGSSTENSAFQQTRNPWNLERVPGGSSGGSAAAVAAGEAPAALGTDTGGSIRQ 181 N F+ N T NPW+ PGGSSGG+A AVA G P A G D GGSIR Sbjct: 146 SNTPCFSFSWDARNDLHGTTWNPWSRAHTPGGSSGGAACAVATGMVPLAHGNDIGGSIRH 205 Query: 182 PAALCGITGLKPTYGRVSRYGLVAFASSLDQI--------GPMARTVRDCAIVLRVIAGA 233 PA CG+ GL+PT GRV GL + A + + GP+AR V D ++L + G Sbjct: 206 PAYCCGVAGLRPTPGRVP--GLFSPAKGDEALGLQLMLVDGPIARGVADLRLMLESMTGF 263 Query: 234 DPFDATCTDYPAPDYEAALTGDIRGLRIGVPREYFVAGMQPDVEAAVRTAIEVLREQGAE 293 DP P P + L + G RIGV RE V P V AA+ A+ L++ G Sbjct: 264 DPRVPGSLPLPLPFPASPL---LPGTRIGVLREDDVKPRTPTVAAALERAVVALQQAGFT 320 Query: 294 VCEISLPHTPYALPVYYLIAPAEASANLARFDGVRYGLRVPGESYFDELERTRGAGFGPE 353 V E+ LP A +++L+ E A L + R G P +++ GF + Sbjct: 321 VEEVRLPELAEAWRLWWLLVMEETRALLPSIE--RDG-DAPIKAWI---------GFNYD 368 Query: 354 VRRRIMLGTYALSAGYYDAYYKRAQQVRTLIRRDYQQAFEQVDVIAAPTTPTVAFKIGAH 413 V M G Y + Y +RA+ + +L QQ + VI P FK G H Sbjct: 369 VASE-MWGRQPSLTDYINGYARRARLIASL-----QQKLRRYPVILMPVASEEPFKQGQH 422 Query: 414 TDDPLAMYLEDVCTLPL---NLAGLPGLVVPCGFAEGLPIGLQLIGRAFDEESLLRVGDA 470 D + PL + G P L VP G +GLP G+QL+GR F E +L+VG A Sbjct: 423 YADLASARAAIASGWPLMAIPVLGFPALAVPTGCVDGLPTGVQLMGRRFHERDVLQVGAA 482 Query: 471 YQRVTDWHTRMPEVR 485 + T M +R Sbjct: 483 LEAAMPVLTPMDPLR 497 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: 622 Number of extensions: 41 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: 490 Length of database: 498 Length adjustment: 34 Effective length of query: 456 Effective length of database: 464 Effective search space: 211584 Effective search space used: 211584 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: 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