Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_086510693.1 BZY95_RS14880 glutamate--ammonia ligase
Query= reanno::pseudo1_N1B4:Pf1N1B4_2254 (426 letters) >NCBI__GCF_002151265.1:WP_086510693.1 Length = 468 Score = 108 bits (271), Expect = 3e-28 Identities = 112/424 (26%), Positives = 178/424 (41%), Gaps = 67/424 (15%) Query: 48 IGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHE---LEGDPFFADPREVLRQVVAKFDE 104 I ++D I P T +P+ + T + + E ++G + DPR + ++ A Sbjct: 60 INESDMILRPEDGTAFLDPFTEDATLVVRCDIIEPATMQG--YERDPRSIAKRAEAYLQS 117 Query: 105 MGLTICAAF--ELEFYLIDQ--------------ENVNGRPQPPRSPISGKRPHSTQV-- 146 GL A F E EF++ DQ + G R G H +V Sbjct: 118 TGLGDTAFFGPEPEFFIFDQVHWKADIEGAMYKITSEEGAWSTDRQLEGGNLGHRPRVKG 177 Query: 147 --YLIDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADP--------- 195 + + +D + D + GA + E+ EV+ H V++ Sbjct: 178 GYFPVPPVDSFHD-----IRGAMCNTL-------EAIGQTVEVHHHEVSNAGQNEIGVKF 225 Query: 196 ---IKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFAS 252 +K D LK +I N+A+ + TFM KP G G+G+HVH S KDG+N FA Sbjct: 226 NTLVKKADEVQELKYVIHNVAHAYGKTATFMPKPLVGDNGSGMHVHQSFW-KDGQNQFAG 284 Query: 253 EDPEQNAALR----HAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTV 308 +Q A L + IGG+++ A AF + NSY+R F P + NR+ Sbjct: 285 ---DQYAGLSEMALYYIGGIIKHARALNAFTNASTNSYKRLVPGFEAPVMLAYSARNRSA 341 Query: 309 AIRVP-TGSSDAVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPGAPVEGNSYE--- 364 +IR+P T S RIE R ANPYL +++L G+ NKI PG ++ N Y+ Sbjct: 342 SIRIPYTASPKGKRIEARFPDPTANPYLAFSAMLMAGIDGIKNKIHPGDAMDKNLYDLPP 401 Query: 365 ---QNEQSLPNNLRDALRELDDSEVM---AKYIDPKYIDIFVACKESELEEFEHSISDLE 418 + ++ ++L AL LD ID ++ K ++E + +E Sbjct: 402 EEGKKVPTVAHSLDQALEALDKDRAFLTEGGVFTDDMIDAYIELKMEDVERIRMTTHPIE 461 Query: 419 YNWY 422 ++ Y Sbjct: 462 FDMY 465 Lambda K H 0.318 0.137 0.411 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: 518 Number of extensions: 27 Number of successful extensions: 3 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: 426 Length of database: 468 Length adjustment: 33 Effective length of query: 393 Effective length of database: 435 Effective search space: 170955 Effective search space used: 170955 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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