Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate SMc01594 SMc01594 hypothetical protein
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__Smeli:SMc01594 Length = 454 Score = 428 bits (1100), Expect = e-124 Identities = 232/451 (51%), Positives = 296/451 (65%), Gaps = 5/451 (1%) Query: 10 AWTELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDL 69 ++ EL+ VAAG +DTV+ DMQGRL GKR +FV+ A + C+YLLA D+++ Sbjct: 4 SFEELKEDVAAGRIDTVLACQVDMQGRLMGKRFHAEYFVES-AWKETHSCNYLLATDMEM 62 Query: 70 NTVPGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLVWADG-SEVAVSPRSIL 128 TVPGY SW+ GYGD M PDLSTLR IPWL GTALV+ D++ D +EV SPR+IL Sbjct: 63 ETVPGYKATSWEKGYGDYTMKPDLSTLRRIPWLEGTALVLCDMLDHDTHAEVPHSPRAIL 122 Query: 129 RRQLDRLKARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSRMEP 188 ++Q+ RL+A G A +A+ELEF +FDQ Y A SGYR L AS YN DY I +++ E Sbjct: 123 KKQVARLEAMGFKAYMASELEFFLFDQSYDDARLSGYRDLQLASGYNEDYHIFQTTKEED 182 Query: 189 LLRDIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGK 248 ++R IR G+ GAG+ E KGE + GQ+EI RY +AL D HAI KNG KEIA Q GK Sbjct: 183 VMRAIRNGLQGAGIPVENSKGEASAGQEEINVRYADALTMADRHAIIKNGCKEIAWQRGK 242 Query: 249 SLTFMAKYD-EREGNSCHIHVSLRGTDG-SAVFADSNGPHGMSSMFRSFVAGQLATLREF 306 ++TF+AK++ G+S HIH SL DG + +F D NG +GMS + R +VAGQLA E Sbjct: 243 AITFLAKWNYSAAGSSSHIHQSLWSKDGETPLFFDKNGQYGMSELMRHYVAGQLAHASEV 302 Query: 307 TLCYAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHGQN-IRVECRVPGGDVNQYL 365 T AP INSYKRF +FAPT W DNRT R+ G G IR+ECRV G D+N YL Sbjct: 303 TYFLAPYINSYKRFMAGTFAPTKAIWSKDNRTAGYRLCGEGSKAIRIECRVGGSDLNPYL 362 Query: 366 AVAALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGED 425 A AALIA G+ GIE ++L P VG+AYQG +V +P TL +A S ++R AFGE+ Sbjct: 363 AFAALIAAGIAGIENKMELEAPFVGDAYQGKEVREIPHTLREAGEALSGSKMLRAAFGEE 422 Query: 426 VVAHYLNNARVELAAFNAAVTDWERIRGFER 456 VV HY++ A E ++ VTDWE RGFER Sbjct: 423 VVDHYVHAAEWEQQEYDRRVTDWEVARGFER 453 Lambda K H 0.321 0.137 0.417 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: 613 Number of extensions: 24 Number of successful extensions: 6 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: 457 Length of database: 454 Length adjustment: 33 Effective length of query: 424 Effective length of database: 421 Effective search space: 178504 Effective search space used: 178504 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 (21.9 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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