Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate GFF2676 PGA1_c27180 putative glutamine synthetase
Query= reanno::MR1:200446 (451 letters) >FitnessBrowser__Phaeo:GFF2676 Length = 450 Score = 176 bits (445), Expect = 2e-48 Identities = 114/374 (30%), Positives = 191/374 (51%), Gaps = 13/374 (3%) Query: 74 DFVCVPDENAVFMLPWTIEATAQVIHDCYDRMGNP-IELSPRNVLKKVLSLYDEKGWEPV 132 D+V PD + +PW +E T V+ D D + + SPR +LK+ ++ E G++ + Sbjct: 78 DYVMKPDLATLRPVPW-LEGTVMVLCDVLDHHSHEEVPHSPRAILKRQVNRLKEMGFDAM 136 Query: 133 IAPEMEFYLTSRSDDHDLPLKPPIGRSGRPEAG-RQSFSIDAANEYDPLFEDMYDWCEIQ 191 A E+EF+L +S D ++ R P +G + +SI + + + + + Sbjct: 137 CATELEFFLFEKSFD---AIRKSGFRDLEPISGYNEDYSILQTSREEHVLRPIRNHLWDA 193 Query: 192 GLDIDTLIHEDGPAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVCATFMAKPVTDE 251 GL I+ E Q E+N + + A + K ++E A + TF+ K ++ Sbjct: 194 GLPIENSKGEAETGQEELNIKYAAAMDTAAYHTIAKHAVKEIAQQQGHAVTFLPKWSHEK 253 Query: 252 PGSAMHIHQSVINKETGKNIFTNEDGT--QSALFLSYIAGLQKYIPEFLPLMAPNANSFR 309 GS+ H+HQS+ + GK F +E S+L +Y+AGL KY P++ MAP NS++ Sbjct: 254 VGSSSHVHQSLW--QDGKPAFFDESDALGMSSLMKAYMAGLLKYAPDYTAFMAPYINSYK 311 Query: 310 RFLPGTSAPVNLEWGIENRTCGLRIPESSPQNRRIENRIPGADANCYLAFAAGLLCGYIG 369 RF+ GT AP + W ++NRT G R+ + R+E RIPG+D N YLA A L G G Sbjct: 312 RFMKGTFAPTRIIWSVDNRTAGYRLCGVGSKAIRVECRIPGSDMNPYLAIAGMLAAGIAG 371 Query: 370 MVEGLKPSTPVQGKANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESFTTGFVAVKQ 429 + EGL+ P G + + +P TL +A A++ S + +G++ +V + Sbjct: 372 IEEGLELQAPTTGDVYQGDTG---MIPGTLRDAATALKSSAMLRAAMGDAVVDHYVRAAE 428 Query: 430 AELENFRRVVSSWE 443 E+E+F R+V+ +E Sbjct: 429 VEIEDFERIVTDYE 442 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: 466 Number of extensions: 17 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: 451 Length of database: 450 Length adjustment: 33 Effective length of query: 418 Effective length of database: 417 Effective search space: 174306 Effective search space used: 174306 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