Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate PfGW456L13_3221 glutamine synthetase family protein
Query= reanno::MR1:200446 (451 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3221 Length = 452 Score = 669 bits (1725), Expect = 0.0 Identities = 323/450 (71%), Positives = 374/450 (83%), Gaps = 3/450 (0%) Query: 2 NKLIAFLKERKITEVECVICDMTGIARGKIAPVDKFLDEKGMRLPESVLLQTVTGDFVDD 61 ++L +LK+ KITEVECV+ D+TGIARGKIAP +KFL E+GMRLPESVLLQTVTGDFVDD Sbjct: 6 DQLFTWLKDHKITEVECVVSDLTGIARGKIAPTNKFLHERGMRLPESVLLQTVTGDFVDD 65 Query: 62 DIYYSLLDDADIDFVCVPDENAVFMLPWTIEATAQVIHDCYDRMGNPIELSPRNVLKKVL 121 DIYY LLD ADID VC PD +AV+++PW IE TA VIHD +D+ GNPIELSPRNVLKKVL Sbjct: 66 DIYYDLLDPADIDMVCKPDADAVYVVPWAIEPTAIVIHDTFDKFGNPIELSPRNVLKKVL 125 Query: 122 SLYDEKGWEPVIAPEMEFYLTSRSDDHDLPLKPPIGRSGRPEAGRQSFSIDAANEYDPLF 181 LY +KGW P++APEMEFYLT R +D DLPLK P+GRSGR E+GRQSFSIDAANE+DPLF Sbjct: 126 QLYTDKGWRPIVAPEMEFYLTQRCEDPDLPLKAPMGRSGRAESGRQSFSIDAANEFDPLF 185 Query: 182 EDMYDWCEIQGLDIDTLIHEDGPAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVCA 241 ED+YDWCE+QGLD+DTLIHEDGPAQMEINF HGN L LADQ+ VFKRT+REAALKHNV A Sbjct: 186 EDVYDWCELQGLDLDTLIHEDGPAQMEINFRHGNALDLADQITVFKRTMREAALKHNVAA 245 Query: 242 TFMAKPVTDEPGSAMHIHQSVINKETGKNIFTNEDGTQSALFLSYIAGLQKYIPEFLPLM 301 TFMAKPV DEPGSAMH+HQSV++ TG+ IF + DG S LFL +I GLQKYIP+ LP+ Sbjct: 246 TFMAKPVGDEPGSAMHLHQSVVDIATGQPIFADADGNMSELFLHHIGGLQKYIPKVLPMF 305 Query: 302 APNANSFRRFLPGTSAPVNLEWGIENRTCGLRIPESSPQNRRIENRIPGADANCYLAFAA 361 APN NSFRRFLP TSAPVN+EWG ENRT GLR+P SSP R+ENR+PGADAN YLA AA Sbjct: 306 APNVNSFRRFLPDTSAPVNVEWGEENRTVGLRVPTSSPDAMRVENRLPGADANPYLAIAA 365 Query: 362 GLLCGYIGMVEGLKPSTPVQGKANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESFT 421 LLCGY+GMVE ++PS VQG+A E R+ LP+T+E+AL MEE YLG F Sbjct: 366 SLLCGYLGMVERIEPSAAVQGRAYERRNLR---LPITIEDALTQMEECVTIGRYLGSKFV 422 Query: 422 TGFVAVKQAELENFRRVVSSWEREFLLLSV 451 G+VAVK+AE ENF+RV+SSWEREFL+LSV Sbjct: 423 RGYVAVKRAEHENFKRVISSWEREFLMLSV 452 Lambda K H 0.319 0.137 0.414 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: 698 Number of extensions: 18 Number of successful extensions: 2 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: 451 Length of database: 452 Length adjustment: 33 Effective length of query: 418 Effective length of database: 419 Effective search space: 175142 Effective search space used: 175142 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 (21.7 bits) S2: 51 (24.3 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