Align Putative asparagine synthetase [glutamine-hydrolyzing] 1; EC 6.3.5.4 (uncharacterized)
to candidate WP_013644771.1 METBO_RS05895 asparagine synthetase B
Query= curated2:Q58516 (541 letters) >NCBI__GCF_000191585.1:WP_013644771.1 Length = 495 Score = 320 bits (820), Expect = 8e-92 Identities = 221/539 (41%), Positives = 307/539 (56%), Gaps = 65/539 (12%) Query: 1 MCSISGII-VKDNQISAKYSIDMMKILKHRGRDNSGLLLDDEVIYFNDFEDVEDLEEEMI 59 MC+I+GI+ + Q + I M+K ++HRG D S + LD +++ D E DL Sbjct: 1 MCAIAGILSINGKQALGEDLICMLKTMEHRGPDGSRICLDGKLVT-GDLETT-DLP---F 55 Query: 60 GNLSLAHNRLAIVGRYGVQPIPNEDETIWLVCNGEIYNYIELREYLKQNHEFRTDSDNEV 119 N+ L HN L+IVG QP+ + LV N EIYNY EL+ + + + TDSD EV Sbjct: 56 ANIGLGHNLLSIVGTEVSQPLVKHG--LVLVANAEIYNYRELKNFYDEC--YFTDSDCEV 111 Query: 120 IIHLYEE-----------EKLEELDGDYAFAIYDKSKNVVRLARDMFGVKPLFYVDRDK- 167 I+ L + ++ELDGDYAFAI + + VV RD GVKP++Y K Sbjct: 112 ILTLVNKYYKNSLVDAVNTTIKELDGDYAFAISNGKELVV--VRDELGVKPVYYATDHKR 169 Query: 168 -YFAFASERKALWHLLINIDGCERDLDELNSKIKTLKPNSQLIYYLDDNRFEIIEGFKKL 226 FAFASERKALW L I + + + + KP ++ N + E F + Sbjct: 170 DLFAFASERKALWKLGIKDVNVLKPGEMILNNKTISKPQTKKKTMPIPNVRDGNESFPQY 229 Query: 227 ELNYMKERSYEEAKEYLDRALKNSVLKRVRGLDKVGIICSGGVDSSLIAKLAS-LYCEVI 285 NY K L + L +SV KRV GLD+VGII SGG+DSS++AKL+ L E Sbjct: 230 GSNYYKN--------LLKKVLIDSVKKRVVGLDRVGIIFSGGLDSSILAKLSKDLEVETF 281 Query: 286 LYAVGTENSEDLIYAERLAKDLNLKLRKKIISEEEYEEYVFKVAKAIDEVDLMKIGVGIP 345 LY VGTENS D+ YA+++A L+L L+ KI++ ++ + Y V AI+E ++MKIGVG+P Sbjct: 282 LYTVGTENSSDMKYAKQVANSLDLPLKSKIVALDDIKHYTGLVLNAIEEYNVMKIGVGMP 341 Query: 346 IYVASEMANEDGLKVVLSGQGADELFGGYARHERIYRERGEEELKKELLKDVYNLYKVNL 405 Y+ASE+A++DG++V+LSGQGADE+F GY R+ + Y+E G E+ + L DV NLY VNL Sbjct: 342 SYIASELASQDGIRVMLSGQGADEIFAGYQRYTQFYQEYG-EKTTEYLEADVSNLYHVNL 400 Query: 406 ERDDHCTMANGVELRVPFLDEEVVEIALSIPIEYKMSELSNRPYAESNISLKSEPINGLK 465 +RDD TMAN VELRVP+LD +VV + L+IP++YK+ +P Sbjct: 401 QRDDAVTMANSVELRVPYLDSKVVNVGLNIPMKYKLGH---------------DP----- 440 Query: 466 NTNLNIKCVRSVRKKILRDVASQY-LPDYIAYRPKKAAQYGSGGEKMIYKVAKKYGFSK 523 +RK ILR +A +P RPKKAAQYGSG +++ K K G K Sbjct: 441 ---------DDLRKCILRRLALDLEVPMEAVLRPKKAAQYGSGIHRLLVKKVLKDGSYK 490 Lambda K H 0.318 0.138 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: 731 Number of extensions: 38 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 541 Length of database: 495 Length adjustment: 35 Effective length of query: 506 Effective length of database: 460 Effective search space: 232760 Effective search space used: 232760 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 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