Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate PP_3148 PP_3148 putative Glutamine synthetase
Query= reanno::MR1:200446 (451 letters) >FitnessBrowser__Putida:PP_3148 Length = 452 Score = 676 bits (1744), Expect = 0.0 Identities = 324/450 (72%), Positives = 381/450 (84%), Gaps = 3/450 (0%) Query: 2 NKLIAFLKERKITEVECVICDMTGIARGKIAPVDKFLDEKGMRLPESVLLQTVTGDFVDD 61 ++L +LKE +ITEVECVI D+TGIARGKIAP KFL E+GMRLPESVLLQTVTGD+VDD Sbjct: 6 DQLSTWLKEHRITEVECVISDLTGIARGKIAPTAKFLHERGMRLPESVLLQTVTGDYVDD 65 Query: 62 DIYYSLLDDADIDFVCVPDENAVFMLPWTIEATAQVIHDCYDRMGNPIELSPRNVLKKVL 121 DIYY+LLD ADID VC PD AV+ +PW IE TA VIHD +D+ GNPIELSPRNVLKKVL Sbjct: 66 DIYYNLLDAADIDMVCRPDPTAVYQIPWAIEPTAIVIHDTFDKQGNPIELSPRNVLKKVL 125 Query: 122 SLYDEKGWEPVIAPEMEFYLTSRSDDHDLPLKPPIGRSGRPEAGRQSFSIDAANEYDPLF 181 LY +KGW+P++APEMEFYLT R +D DLPL+ P+GRSGR E+GRQSFSIDAANE+DPLF Sbjct: 126 KLYADKGWQPIVAPEMEFYLTKRCEDPDLPLQVPLGRSGRAESGRQSFSIDAANEFDPLF 185 Query: 182 EDMYDWCEIQGLDIDTLIHEDGPAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVCA 241 ED+YDWCEIQGLD+DTLIHEDGPAQMEINF HG+ L LADQ+ VFKRT+REAALKHNV A Sbjct: 186 EDVYDWCEIQGLDLDTLIHEDGPAQMEINFRHGDALDLADQITVFKRTMREAALKHNVAA 245 Query: 242 TFMAKPVTDEPGSAMHIHQSVINKETGKNIFTNEDGTQSALFLSYIAGLQKYIPEFLPLM 301 TFMAKP+TDEPGSAMH+HQSV++ TGK IF NEDG+ S LFL +I GLQKYIP+ LP+ Sbjct: 246 TFMAKPITDEPGSAMHLHQSVVDIATGKPIFANEDGSMSQLFLHHIGGLQKYIPKLLPMF 305 Query: 302 APNANSFRRFLPGTSAPVNLEWGIENRTCGLRIPESSPQNRRIENRIPGADANCYLAFAA 361 APN NSFRRFLP TSAPVN+EWG ENRT GLR+P SSP+ R+ENR+PGADAN YLA AA Sbjct: 306 APNVNSFRRFLPDTSAPVNVEWGEENRTAGLRVPTSSPEAMRVENRLPGADANPYLAIAA 365 Query: 362 GLLCGYIGMVEGLKPSTPVQGKANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESFT 421 LLCGY+GMVE + PS PVQG+A E R+ LP+T+E+AL ME+ + ++YLG+ F Sbjct: 366 SLLCGYLGMVEQIDPSAPVQGRAYERRNLR---LPITIEDALQHMEDCETVQQYLGKQFV 422 Query: 422 TGFVAVKQAELENFRRVVSSWEREFLLLSV 451 G+VAVK+AE EN++RV+SSWEREFL+LSV Sbjct: 423 QGYVAVKRAEHENYKRVISSWEREFLMLSV 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: 684 Number of extensions: 23 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