Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate PfGW456L13_3221 glutamine synthetase family protein
Query= BRENDA::P36687 (439 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3221 Length = 452 Score = 186 bits (473), Expect = 1e-51 Identities = 136/432 (31%), Positives = 206/432 (47%), Gaps = 39/432 (9%) Query: 11 DSKIKFVQLVFVDINGMPKG-------------MEIPASRLEEAVTDGISFDGSSVPGFQ 57 D KI V+ V D+ G+ +G M +P S L + VT G D Sbjct: 14 DHKITEVECVVSDLTGIARGKIAPTNKFLHERGMRLPESVLLQTVT-GDFVDDDIYYDLL 72 Query: 58 GIEDSDLVFKADPDTYVEVPW---DNVARVYGFIYKDNKPYGADPRGILKRALEELEKEG 114 D D+V K D D VPW ++ K P PR +LK+ L+ +G Sbjct: 73 DPADIDMVCKPDADAVYVVPWAIEPTAIVIHDTFDKFGNPIELSPRNVLKKVLQLYTDKG 132 Query: 115 YKAYIGPEPEFYLFKKNGTWELEIPDVGGY----------FDILTLDKARDIRREIAEYM 164 ++ + PE EFYL ++ +L + G F I ++ + ++ ++ Sbjct: 133 WRPIVAPEMEFYLTQRCEDPDLPLKAPMGRSGRAESGRQSFSIDAANEFDPLFEDVYDWC 192 Query: 165 PSFGLIPEVLHHEVGKAQHEIDFRYDEALKTADNIVSFKYITKAVAEMHGLYATFMPKPL 224 GL + L HE G AQ EI+FR+ AL AD I FK + A H + ATFM KP+ Sbjct: 193 ELQGLDLDTLIHEDGPAQMEINFRHGNALDLADQITVFKRTMREAALKHNVAATFMAKPV 252 Query: 225 FGFPGNGMHLHISLSK--DGENVFMGEEG-LSEIALHFIGGILKHAKALIAVTNPTVNSY 281 PG+ MHLH S+ G+ +F +G +SE+ LH IGG+ K+ ++ + P VNS+ Sbjct: 253 GDEPGSAMHLHQSVVDIATGQPIFADADGNMSELFLHHIGGLQKYIPKVLPMFAPNVNSF 312 Query: 282 KRLVPGYEAPVYISWGYRNRSALIRVPAFWGKGARIEYRCPDPSANPYFAFAAVLKAGLD 341 +R +P APV + WG NR+ +RVP R+E R P ANPY A AA L G Sbjct: 313 RRFLPDTSAPVNVEWGEENRTVGLRVPTSSPDAMRVENRLPGADANPYLAIAASLLCGYL 372 Query: 342 GIKHKIDPFAYVEENVYEMSEEKRKELGIETLPGSLGEALEELEKDKVVKEALGDAY-KN 400 G+ +I+P A V+ YE R+ L LP ++ +AL ++E+ + LG + + Sbjct: 373 GMVERIEPSAAVQGRAYE-----RRNL---RLPITIEDALTQMEECVTIGRYLGSKFVRG 424 Query: 401 FINYKWKEWESY 412 ++ K E E++ Sbjct: 425 YVAVKRAEHENF 436 Lambda K H 0.318 0.139 0.419 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: 511 Number of extensions: 24 Number of successful extensions: 4 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: 439 Length of database: 452 Length adjustment: 32 Effective length of query: 407 Effective length of database: 420 Effective search space: 170940 Effective search space used: 170940 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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