Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate CA265_RS24865 CA265_RS24865 glutamine synthetase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__Pedo557:CA265_RS24865 Length = 453 Score = 202 bits (513), Expect = 2e-56 Identities = 145/453 (32%), Positives = 217/453 (47%), Gaps = 22/453 (4%) Query: 3 DIDDFLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQA-VMIQTVTGDYP-E 60 +I D++K + +++ + D+ GI RGK + KF S RL V GD E Sbjct: 6 EILDYVKNHPSGKVKLAVADIDGILRGKYVAAEKFASLVEGRLGFCDVTFGWDAGDVAYE 65 Query: 61 DGTLTG--VTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVL 118 +G TG PD D +T R IPW + + D ++ P A+ PR++L++V+ Sbjct: 66 NGKYTGWHTGYPDAQVKIDLTTFRKIPWE-NEVPFFLGDFINDQDQPNAVCPRQLLKKVI 124 Query: 119 ELYKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLF 178 + +G+ P+ A E E++ + ++ P+ + G YSI + Sbjct: 125 TECENEGFSPLFAQEFEWF--NFSETPESIHEKGFANLKPLSPGMFGYSILRSTYRNEFM 182 Query: 179 EDIYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYA 238 D+++ ++ ++ L E G E + L+ AD LFK V+E A +H + A Sbjct: 183 SDLFDLLNKFDIPIEGLHTETGPGVYEAAIKYAPALQAADQAILFKTAVKEIAYKHGILA 242 Query: 239 TFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTGPD--GKPTSLFTSYIAGLQKYTPALMP 296 TFMAK E PG + H+HQSL D + NLF + + SYIAG P L+P Sbjct: 243 TFMAKISENLPGCSGHVHQSLWDADKKTNLFYDEKDAAQMSDTMKSYIAGQLHCLPYLLP 302 Query: 297 IFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAI 356 + AP INSY+RL AP V WG DNRT R A R+E RI G D NPYLA+ Sbjct: 303 MIAPTINSYKRLVEGAWAPTTVTWGIDNRTTALRALPGSKKASRLETRIVGSDTNPYLAL 362 Query: 357 AATLAAGYLGMTQKLEATEPL--------LSDGYELPYQLPRNLEEGLTLMGACEPIAEV 408 +A LAAG G+ KL+ + LS+G L RNL E M + A + Sbjct: 363 SACLAAGMFGVKNKLKLNQAATKGNGYTDLSNGV-----LSRNLFEATQKMKNSDLAATL 417 Query: 409 LGEKFVKAYLALKETEYEAFFRVISSWERRHLL 441 LG+ FV + +E E + + +V++ WE + L Sbjct: 418 LGKDFVDHFTMTREWECKQYAKVVTDWELKRYL 450 Lambda K H 0.321 0.138 0.418 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: 504 Number of extensions: 24 Number of successful extensions: 5 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: 444 Length of database: 453 Length adjustment: 33 Effective length of query: 411 Effective length of database: 420 Effective search space: 172620 Effective search space used: 172620 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 (21.8 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