Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_011382566.1 AMB_RS00600 asparagine synthase (glutamine-hydrolyzing)
Query= BRENDA::P22106 (554 letters) >NCBI__GCF_000009985.1:WP_011382566.1 Length = 639 Score = 152 bits (384), Expect = 4e-41 Identities = 131/395 (33%), Positives = 189/395 (47%), Gaps = 59/395 (14%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVNAGA 60 MC IFG+ VE A + + HRGPD +GI+A L + RL++VD G+ Sbjct: 1 MCGIFGMVRGGGRPVESNVLAA-MKTALHHRGPDGNGIFAEGPVGLGNTRLAVVDTAGGS 59 Query: 61 QPLYNQQKTHVLAVNGEIYNHQALRAEYGD-RYQFQTGSDCEVILALYQEKGPEFLDDLQ 119 QP+ + + NGE++NH LRAE + F+T SD EV+LA + G + + Sbjct: 60 QPVIDPSSGAAIVYNGELFNHLELRAELESVGWCFRTHSDTEVVLAAFCVWGEDCVLRFN 119 Query: 120 GMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKALVPVCRT-------- 171 GM+AFA++D + I RD GI PLY+ G L ASE KAL+P+ Sbjct: 120 GMYAFAVFDPKARRVFIARDPAGIKPLYLTETADG-LAFASEAKALLPIAGRRPDWQALW 178 Query: 172 -----------------IKEFPAGSYLWSQDGEIRSY------YHRDWFDYDAVKDNVTD 208 I +FPAGS W D E+ + Y + F A Sbjct: 179 GYLTYGYMAPDCSPFAGITKFPAGSLAWI-DLELPAARLAVRPYWQPRFGCGAPLAEGEA 237 Query: 209 KNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQL 268 + L L +VK LMSDVP G+ LSGGLDSS ++ YAARR +A + Sbjct: 238 VDRLDALLSQAVKHELMSDVPVGLFLSGGLDSSAVA----YYAARR-----HGQA----I 284 Query: 269 HSFAVGLPGS--PDLKAAQEVANHLGTVHHEIHFT---VQEGLDAIRDVIYHIETYDVTT 323 SF + + + A+ VA HLG H E+ F+ V+EGL + + + E + +T Sbjct: 285 SSFGLAFEETTHDESNDARTVARHLGIEHKELMFSPALVREGLRRVTETM--DEPFGDST 342 Query: 324 IRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGY 358 + P+ ++SR + + +VL+G G DEV GY Sbjct: 343 V---VPLLMLSRFARE-HVTVVLTGWGGDEVLAGY 373 Score = 39.7 bits (91), Expect = 4e-07 Identities = 25/82 (30%), Positives = 43/82 (52%), Gaps = 3/82 (3%) Query: 381 LHMYDCARANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAY 440 LH +A++ A +EARVP L+K+ LD A+ + KM G K +L++ + Sbjct: 490 LHGNGLFQADRMTMAASLEARVPLLNKQMLDFALPLPAGLKMAGG--TPKGLLKKALAPH 547 Query: 441 LPASVAWRQKEQFSDGVGYSWI 462 LP ++ + K+ F G+ W+ Sbjct: 548 LPPAILSKPKKGFGPPSGH-WV 568 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: 812 Number of extensions: 43 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 554 Length of database: 639 Length adjustment: 37 Effective length of query: 517 Effective length of database: 602 Effective search space: 311234 Effective search space used: 311234 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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