Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate GFF1957 HP15_1914 asparagine synthase, glutamine-hydrolyzing
Query= BRENDA::P22106 (554 letters) >FitnessBrowser__Marino:GFF1957 Length = 632 Score = 147 bits (371), Expect = 1e-39 Identities = 122/394 (30%), Positives = 188/394 (47%), Gaps = 56/394 (14%) Query: 1 MCSIFGVFDIKT--DAVELRKKALELSRLMRHRGPDWSGIYASDNAILAHERLSIVDVN- 57 MC I G T D + A + + + HRGPD +G++ + L H+RLSI+D++ Sbjct: 1 MCGIAGFLRTGTLPDREQHHLWAERMGQAIAHRGPDANGVHIDQDVALVHQRLSILDLSS 60 Query: 58 AGAQPLYNQQKTHVLAVNGEIYNHQALRAEYG-DRYQFQTGSDCEVILALYQEKGPEFLD 116 AG QP+ + +++ NGEIYN ++LR D + F+T +D EV+LALY G L Sbjct: 61 AGNQPMASSCGRYIIVFNGEIYNFRSLREGLEQDGFSFKTQTDTEVLLALYARHGESCLR 120 Query: 117 DLQGMFAFALYDSEKDAYLIGRDHLGIIPLYMGYDEHGQLYVASEMKAL--VPVCR---- 170 L GMFAFA++D++ + IGRD LG PLY D GQ + SE+KAL PV R Sbjct: 121 QLNGMFAFAIWDAKTKSLFIGRDRLGKKPLYY-TDTDGQFFFGSEIKALFATPVVRPALR 179 Query: 171 --TIKEF-------------------PAGSYLWSQDGEIRSYYHRDWFDYDAVKDNVTD- 208 IK+F P G + +G I + D V+D Sbjct: 180 PDAIKDFFVYQYIPDPKTIYANVHKLPPGHCMEVCEGRISVRKYWDLSFRPVEGRTVSDI 239 Query: 209 KNELRQALEDSVKSHLMSDVPYGVLLSGGLDSSIISAITKKYAARRVEDQERSEAWWPQL 268 K L ++++V+ ++SDVP G LSGG+DSS + + +++ V Sbjct: 240 KAGLYDVIDEAVRLRMISDVPLGAFLSGGIDSSAVVGLMAGRSSQPVT------------ 287 Query: 269 HSFAVGLPGS--PDLKAAQEVANHLGTVHHEIHFTVQEGLDAIRDVIYHIETY--DVTTI 324 + +G ++K A VA T HH FTV+E + D + I + + Sbjct: 288 -TCTIGFDDEKFDEIKYADLVARQFKTDHHV--FTVKE---TVADNLVGISRFFDEPFAD 341 Query: 325 RASTPMYLMSRKIKAMGIKMVLSGEGSDEVFGGY 358 + P + +S+ + + + L+G+G DE F GY Sbjct: 342 PSFVPTFFVSQLARTQ-VTVALAGDGGDENFAGY 374 Score = 41.2 bits (95), Expect = 1e-07 Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 2/67 (2%) Query: 388 RANKAMSAWGVEARVPFLDKKFLDVAMRINPQDKMCGNGKMEKHILRECFEAYLPASVAW 447 + ++ A +E R P LD + ++ A I K+ GN K KH+L+ECF L + + Sbjct: 497 KVDRMSMANSLETRAPLLDYRVVEYAAGIPSALKLKGNCK--KHVLKECFSDLLDEDILY 554 Query: 448 RQKEQFS 454 R+K FS Sbjct: 555 RKKMGFS 561 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: 797 Number of extensions: 41 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: 632 Length adjustment: 37 Effective length of query: 517 Effective length of database: 595 Effective search space: 307615 Effective search space used: 307615 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