Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate PP_5183 PP_5183 glutamylpolyamine synthetase
Query= reanno::MR1:200446 (451 letters) >FitnessBrowser__Putida:PP_5183 Length = 452 Score = 690 bits (1780), Expect = 0.0 Identities = 328/451 (72%), Positives = 387/451 (85%), Gaps = 3/451 (0%) Query: 1 MNKLIAFLKERKITEVECVICDMTGIARGKIAPVDKFLDEKGMRLPESVLLQTVTGDFVD 60 +++L +LKE KITEVEC+I D+TGI RGKI+P +KF+ EKGMRLPESVLLQTVTGD+VD Sbjct: 5 LDQLTDWLKEHKITEVECMISDLTGITRGKISPTNKFIAEKGMRLPESVLLQTVTGDYVD 64 Query: 61 DDIYYSLLDDADIDFVCVPDENAVFMLPWTIEATAQVIHDCYDRMGNPIELSPRNVLKKV 120 DDIYY LLD ADID +C PDENAVF++PW IE TAQVIHD YD+ GNP+ELSPRNVLKKV Sbjct: 65 DDIYYELLDPADIDMICRPDENAVFLVPWAIEPTAQVIHDTYDKKGNPVELSPRNVLKKV 124 Query: 121 LSLYDEKGWEPVIAPEMEFYLTSRSDDHDLPLKPPIGRSGRPEAGRQSFSIDAANEYDPL 180 L LY +KGW+P++APEMEFYLT RS+D D PL+PP+GRSGRPE GRQSFSI+AANE+DPL Sbjct: 125 LKLYADKGWQPIVAPEMEFYLTKRSEDPDFPLQPPVGRSGRPETGRQSFSIEAANEFDPL 184 Query: 181 FEDMYDWCEIQGLDIDTLIHEDGPAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVC 240 FED+YDWCE+Q LD+DTLIHEDG AQMEINF HG+ L LADQ+ VFKRT+REAALKHNV Sbjct: 185 FEDVYDWCELQQLDLDTLIHEDGTAQMEINFRHGDALHLADQILVFKRTMREAALKHNVA 244 Query: 241 ATFMAKPVTDEPGSAMHIHQSVINKETGKNIFTNEDGTQSALFLSYIAGLQKYIPEFLPL 300 ATFMAKP+T EPGSAMH+HQSV++ TGKNIF+NEDG+ SALFL++I GLQK+IPE LPL Sbjct: 245 ATFMAKPMTGEPGSAMHLHQSVVDVATGKNIFSNEDGSMSALFLNHIGGLQKFIPEALPL 304 Query: 301 MAPNANSFRRFLPGTSAPVNLEWGIENRTCGLRIPESSPQNRRIENRIPGADANCYLAFA 360 APN NSFRRFLP TSAPVN+EWG ENRT GLR+P++ PQ+RR+ENR+PGADAN YLA A Sbjct: 305 FAPNVNSFRRFLPDTSAPVNVEWGEENRTVGLRVPDAGPQSRRVENRLPGADANPYLAIA 364 Query: 361 AGLLCGYIGMVEGLKPSTPVQGKANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESF 420 A LLCGYIGMVEG++ S PVQG+ E R+ LPLT+E+AL ME S A +YLG+ F Sbjct: 365 ASLLCGYIGMVEGIEASAPVQGRGYERRNLR---LPLTIEDALERMENSRALVQYLGKKF 421 Query: 421 TTGFVAVKQAELENFRRVVSSWEREFLLLSV 451 TG+VA K+AE ENF+RV+SSWEREFLL +V Sbjct: 422 ITGYVATKRAEHENFKRVISSWEREFLLFAV 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: 727 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