Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate WP_110205265.1 DNK54_RS02005 type I glutamate--ammonia ligase
Query= reanno::MR1:200446 (451 letters) >NCBI__GCF_003194585.1:WP_110205265.1 Length = 445 Score = 182 bits (462), Expect = 2e-50 Identities = 132/386 (34%), Positives = 185/386 (47%), Gaps = 20/386 (5%) Query: 74 DFVCVPDENAVFMLPWTIE--ATAQVIHDCYDRMGNPIELSPRNVLKKVLSLYDEKGWEP 131 D + +PD +LPW E +TA++ D G+P PR VLK+ LS EKG+ Sbjct: 66 DMLAMPDPTTFQILPWRGEGPSTARMFCDIVMPDGSPSYADPRYVLKRTLSAAAEKGFTF 125 Query: 132 VIAPEMEFYLTSRSDDHDLPLKP-PIGRSGRPEAGRQSFSIDAANEYDPLFEDMYDWCEI 190 PE+EFYL D + +P P+ RSG + QS+ D E + E M Sbjct: 126 YTHPEIEFYLFK--DTPNSTAEPVPVDRSGYFDHTAQSYGSDFRREAITMLEAM------ 177 Query: 191 QGLDIDTLIHEDGPAQMEINFSHGNPLSLADQVFVFKRTLREAALKHNVCATFMAKPVTD 250 G+ ++ HE GP Q EI+ + + LS AD + F+ +RE AL + ATFM KP T+ Sbjct: 178 -GISVEFSHHEGGPGQQEIDLRYADALSTADNIMTFRTVVREVALSQGIWATFMPKPFTE 236 Query: 251 EPGSAMHIHQSVINKETGKNIFTNEDGTQSALFLSYIAGLQKYIPEFLPLMAPNANSFRR 310 PGS MH H S+ + + S +IAG+ + E L NS++R Sbjct: 237 HPGSGMHTHVSLFEGDRNAFFEAGAEYQLSQTGRQFIAGVLTHASEITALTNQWVNSYKR 296 Query: 311 FLPGTSAPVNLEWGIENRTCGLRIPESSP---QNRRIENRIPGADANCYLAFAAGLLCGY 367 L G AP + WG NR+ +R+P P Q+ RIE R N YLAFAA L G Sbjct: 297 LLGGGEAPSYICWGHNNRSAMVRVPMYKPNKGQSTRIELRTIDPACNPYLAFAAILGAGM 356 Query: 368 IGMVEGLKPSTPVQG-----KANESRSNNPHCLPLTLEEALVAMEESDACKEYLGESFTT 422 G+ EG + + E +S LP TL EA+ E S+ E LGE Sbjct: 357 KGIEEGYELPREAEDDVWSLNERERQSLGIEPLPKTLYEAIRVAESSELLPEVLGEHVYE 416 Query: 423 GFVAVKQAELENFRRVVSSWEREFLL 448 F+ K+AE + +R VS++ER +L Sbjct: 417 YFLRNKRAEWDEYRVQVSAFERSRML 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: 439 Number of extensions: 27 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: 451 Length of database: 445 Length adjustment: 33 Effective length of query: 418 Effective length of database: 412 Effective search space: 172216 Effective search space used: 172216 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 24 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