Align asparagine synthetase B, glutamine-hydrolyzing; EC 6.3.5.4 (characterized)
to candidate WP_013136341.1 ARNIT_RS12720 asparagine synthase (glutamine-hydrolyzing)
Query= CharProtDB::CH_002444 (554 letters) >NCBI__GCF_000092245.1:WP_013136341.1 Length = 602 Score = 134 bits (337), Expect = 1e-35 Identities = 126/422 (29%), Positives = 204/422 (48%), Gaps = 70/422 (16%) Query: 1 MCSIFGVFDIKTDAVELRKKALELSRLMRHRGPDWSGI----YASDNAILAHERLSIVDV 56 MCSI G F+ E+ K+ + +M HRGPD + + + + N H RLSI D+ Sbjct: 1 MCSILGYFNTALSYSEVVKQ----NSIMVHRGPDDTIVKEYKFLNKNLYFGHNRLSIQDL 56 Query: 57 -NAGAQPLYNQQKTHVLAVNGEIYNHQALRAEYGDRYQFQTGSDCEVILALYQEKGPE-F 114 N QP+ N++ ++ NGEIYNH +R + +F+T SD E IL + E G E Sbjct: 57 ENHANQPMENER--FIIVFNGEIYNHFEIRTQL-QFSKFRTTSDTETILWAFTEFGIEKA 113 Query: 115 LDDLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKAL------VPV 168 ++ GMFA L+D + RD +GI PLY + G+ ASE+K Sbjct: 114 IEQFIGMFAIGLFDKIAQKLYLIRDRVGIKPLYYTMQK-GEFSFASELKGFGEHLKKTTS 172 Query: 169 CRTIKEFPAGSYLWSQDGEIRSYYH--------------------RDWFDYDAVKDNVTD 208 + + +F Y+ + + SYY + ++D K N++ Sbjct: 173 NKALIQFMTLGYIPNDN----SYYDGINKLPPAHYAIFDGVNIDIKKYWDLPEEKINISY 228 Query: 209 KN---ELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWW 265 E Q + S+K L++DV G LSGG+DSS++S+I + QE S+ Sbjct: 229 NEAVKETEQLIRSSIKYRLLADVEVGSFLSGGIDSSLVSSIMQ---------QESSQ--- 276 Query: 266 PQLHSFAVGLPGS--PDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETYDVTT 323 +L +F++G + A+E+A ++G+ H+E F +Q+ + D + YD Sbjct: 277 -KLKTFSIGFEDKFYDESVYAKEIAKYIGSEHYEYKFGIQDVFKLLED---FDKFYDEPF 332 Query: 324 IRAST-PMYLMSRKIKAMGIKMVLSGEGSDEVFGGY-LYFHKAPNAKELHE--ETVRKLL 379 AS+ PM L+S K K + + LSG+G DE+F GY YF K+L + +++R +L Sbjct: 333 GDASSLPMLLLSDKTKDY-VTVALSGDGGDELFLGYDRYFTTESYYKKLKQIPQSLRTIL 391 Query: 380 AL 381 ++ Sbjct: 392 SV 393 Score = 32.7 bits (73), Expect = 4e-05 Identities = 38/176 (21%), Positives = 74/176 (42%), Gaps = 15/176 (8%) Query: 305 GLDAIRDVIYHIETYDVTTIRASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGYLYFHKA 364 G D ++ + Y ++ + A L+ K + + E S E FG Y + Sbjct: 399 GQDKLKKISYPLKQLSEQNLYA-----LLYSSTKPWELNSLFDKEFSRESFGKYEVSLQD 453 Query: 365 PNAKELHEETVRKLLA---LHMY----DCARANKAMSAWGVEARVPFLDKKFLDVAMRIN 417 EL +++ L+ H Y + ++A ++ +EARVP LD + ++ A + Sbjct: 454 ILEYELDGDSLIDSLSRLDFHRYLPDDILTKVDRASMSYSLEARVPLLDHRIVEFAYSLP 513 Query: 418 PQDKMCGNGKMEKHILRECFEAYLPASVAWRQKEQFSDGVGYSWIDTLKEVAAQQV 473 + K+ K IL+E +P + R K FS + + + LK++ ++ Sbjct: 514 IKLKLKHG---PKSILKEILYKEVPKELIERPKRGFSVPLKHWFRKELKDIVYDKI 566 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: 716 Number of extensions: 49 Number of successful extensions: 6 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: 602 Length adjustment: 36 Effective length of query: 518 Effective length of database: 566 Effective search space: 293188 Effective search space used: 293188 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