Align asparagine synthase (glutamine-hydrolysing) (EC 6.3.5.4) (characterized)
to candidate WP_083930282.1 METMI_RS0111890 hypothetical protein
Query= BRENDA::Q14SM9 (569 letters) >NCBI__GCF_000384075.1:WP_083930282.1 Length = 528 Score = 210 bits (534), Expect = 1e-58 Identities = 162/518 (31%), Positives = 257/518 (49%), Gaps = 28/518 (5%) Query: 1 MCGILAVLGCVDNSQTKRARII-ELSRRLRHRGPDWSGIHCYEDCYLAHQRLAIVDPTSG 59 MCGI ++ +N+ ++++ E+ + HRG GI + L RL ++ G Sbjct: 1 MCGIAGIISKPNNADINISKLVNEMLELISHRGRGELGIKTGNNYSLGCYRLPVLT-NGG 59 Query: 60 DQPLYNEDKTVIVTVNGEIYNHKQLRQKLS-SHQFRTGSDCEVIAHLYEEHGEEFVNMLD 118 +QP+ NE K++ +NGEIYN+ +L L H + D ++ HLYEE GE + L Sbjct: 60 EQPVSNELKSIFAVLNGEIYNYNELIDSLKLKHTIKGDCDTVILPHLYEE-GELSLRKLS 118 Query: 119 GMFAFILLDTRDKSFIAARDAIGITPLYLGWGHDGSTWFASEMKALSDDCERFIS-FPPG 177 GM+A + DT + RD IGI PLY+ + ++ FASE KA S +S PG Sbjct: 119 GMYALCVHDTVSNETVLMRDLIGIKPLYI-FENNFFIAFASEKKAFSYLNHGKVSEVMPG 177 Query: 178 HIYSSKQGGLRRWYN--PPWFSEDIPST--PYDPTLLRETFERAVVKRMMTDVPFGVLLS 233 + K G + N PW + D T LR+ ++++++ ++ P VL S Sbjct: 178 ELLRLKHGLITSRANIVKPWNKSLVKGNYQSVDYTGLRDEITNSLIQQLPSEWPVAVLCS 237 Query: 234 GGLDSSLVAAVVNRYLAESESARQWGSQLHTFCIGLKGSPDLKAAKEVADYLGTRHHELY 293 GG+DS ++ + +Y + A + IG + S D+KAA+ +L E+ Sbjct: 238 GGIDSVILTYLAKKYHKHNVQA---------YVIGNENSADVKAARLACHHLDVNLKEIR 288 Query: 294 FTVQEGIDALEEVIYHIETYDVTTIRASTAMFLMSRKIKALGVKMVLSGEGSDEIFGGYL 353 +++E I L EVIYH+E+++ IR S +L+ R+I+ G ++ + GEG+DE+F GY Sbjct: 289 ISMEEIIKVLPEVIYHVESFESNLIRNSILSYLVFREIRKDGFRVAICGEGADELFAGYG 348 Query: 354 YFHKAPNKKEFHEETCRKIKALHLYDCLRANKSTAAWGVEARVPFLDKEFINVAMSIDPE 413 F + E + + L R ++++ A+ VE RVPFLD I A +I P Sbjct: 349 DFRLLSSIIEKQKFMKLLLDDLFKTQLQRVDRTSMAFNVETRVPFLDDNVIEYACNI-PI 407 Query: 414 WKMIRPDLGR-IEKWVLRNAFDDDKNPYLPKHILYRQKEQFSDGVG---YSWIDG-LKDH 468 K D GR + K LR+AF N +P IL RQKE FS G G S + G ++ Sbjct: 408 EKKCGKDFGRWLSKLPLRHAF---ANTQIPTEILLRQKETFSSGAGLGDLSMVGGPIEKI 464 Query: 469 ANKQVTDATMMAANFIYPENTPTTKEGYLYRTIFEKFF 506 A +++ ++ YP T E LY + + K+F Sbjct: 465 AQSRISSNEFISMQSKYPVIDIKTYEQALYLSEYLKYF 502 Lambda K H 0.320 0.136 0.423 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: 592 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 569 Length of database: 528 Length adjustment: 36 Effective length of query: 533 Effective length of database: 492 Effective search space: 262236 Effective search space used: 262236 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