Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate WP_011606722.1 FRAAL_RS24565 asparagine synthase (glutamine-hydrolyzing)
Query= CharProtDB::CH_002444 (554 letters) >NCBI__GCF_000058485.1:WP_011606722.1 Length = 613 Score = 152 bits (383), Expect = 5e-41 Identities = 152/544 (27%), Positives = 227/544 (41%), Gaps = 96/544 (17%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60 MC I G D E + ++ +R RGPD G + +A + H RL+++D+ G Sbjct: 1 MCGITGWVSFGQDDYEQKTVIEAMTATLRRRGPDAGGTWVGAHAAIGHRRLAVIDLVGGV 60 Query: 61 QPLYNQQK--THVLAVNGEIYNHQALRAEYGDR-YQFQTGSDCEVILALYQEKGPEFLDD 117 QP+ + Q VL +GEIYNH LR E R + +T SD EV+L Y E G +D Sbjct: 61 QPMVSDQDGAETVLTYSGEIYNHHELRGELVRRGHTLRTRSDTEVVLHAYLEWGDLLVDR 120 Query: 118 LQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALV--PVCRT---- 171 L+GM+AFA++D L+ RD LG+ PL+ + G + SE KAL P+ R Sbjct: 121 LEGMYAFAVWDERAGRLLLVRDRLGVKPLFYA-EIPGGVVFGSEPKALFCHPLVRPRVNA 179 Query: 172 --IKE-----FPAGSYLWSQDGEI---------------RSYYHRDWFDYDAVKDNVTDK 209 ++E F G +W+ E+ R+Y+ D AV Sbjct: 180 DGLREAYSLLFNTGPTVWTGVRELAPGALATFGPHGLTERTYWALDAAAMAAVSPQAA-V 238 Query: 210 NELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQLH 269 ++R LE + + L +DVP LLSGGLDS++++A+ RR R ++ Sbjct: 239 EQVRVHLERATAAQLEADVPLCSLLSGGLDSTVLTALLADELRRREGPHARIRSFAVDYS 298 Query: 270 SFAVGLPG-----SPDLKAAQEVANHLGTVHHEIHFTVQEGLD-AIRDVIYHIETYDVTT 323 AV G D A E + ++GT H + LD R + + Sbjct: 299 DQAVQFTGDVLRTGHDAPYAVEASRYIGTDHSTVVLDPHTLLDPEHRLAVVAARDSPIGV 358 Query: 324 IRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFH-----KAP------------- 365 T +Y++ KI A + LSGE +DEVFGGY +FH AP Sbjct: 359 GDMDTSLYVLFGKI-AQSSTVALSGEAADEVFGGYPWFHSPAALSAPTFPWLLVTGDEAA 417 Query: 366 -----------NAKELHEETVRKLLAL--HMYD-----------------------CARA 389 +E +T R LA H+ R Sbjct: 418 MPLHPDLAATLRIEEFRADTYRDALAAVPHLDGEDPTEHRQREMAHLSLTRWLRQLLHRK 477 Query: 390 NKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVAWRQ 449 ++ A G+E RVP+ D + ++ A + P +G+ EK +LR P SV R+ Sbjct: 478 DRLSMAQGIEVRVPYCDHRLVEYAFGV-PWAVRSFDGR-EKSLLRAAGAGRCPESVLIRE 535 Query: 450 KEQF 453 K + Sbjct: 536 KNHY 539 Lambda K H 0.319 0.135 0.407 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: 791 Number of extensions: 38 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 554 Length of database: 613 Length adjustment: 36 Effective length of query: 518 Effective length of database: 577 Effective search space: 298886 Effective search space used: 298886 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: 53 (25.0 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