Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate WP_086508337.1 BZY95_RS02000 glutamine synthetase
Query= reanno::Koxy:BWI76_RS10710 (472 letters) >NCBI__GCF_002151265.1:WP_086508337.1 Length = 459 Score = 170 bits (431), Expect = 8e-47 Identities = 137/444 (30%), Positives = 202/444 (45%), Gaps = 32/444 (7%) Query: 39 YVDVLLTDLNGCFRGKRIPVSGL-SKLEKGCYFPASVFAMDILGNVVEEAGL-GQEMGEP 96 +V V + D++G GK + L +G F V D + + G G P Sbjct: 26 HVKVGMFDIDGVMVGKYMRRDKFFHALSEGFAFCDVVLGWDSKDELYDNVTYTGWHTGYP 85 Query: 97 DRTCVPVLGTLTPSAADPEYIGQVLLTMVDEDGAPFDVEPRNVLNRLWQQLRQRGLFPVV 156 D L + S + G +LL + + G ++ PR +L R+ + G Sbjct: 86 DAA----LRLIPESCRELPCEGDMLLFLAEFTGPAGEICPRGLLRRVLAKAEAMGFTACG 141 Query: 157 AVELEFYLLDRKRDAEGYLQPPCAPGTGDRNTQSQV-----YSVDNLNHFADVLNEIDEI 211 A+E EF+L P G RN + YS+ + ++ +E+ + Sbjct: 142 ALEYEFFLFQET--------PESVREKGFRNLKPFTPDMMGYSMLRSSVHGELYHELLGM 193 Query: 212 AQLQLIPADGAVAEASPGQFEINLHHTDNVLDACDDALALKRLVRLMAEKHKMHATFMAK 271 A+ P +G E PG E + D L A D K ++ A++ + ATFMAK Sbjct: 194 AEAMDFPIEGLHTETGPGVLEAAIR-VDEALAAGDKGALFKTFTKVWAQRRGLMATFMAK 252 Query: 272 PYEEHAGSGMHIHISMQN-NKGENVLADADGED--SAMLKRALAGMIDLMPASMALLAPN 328 ++ G HIH+S+ + + GE+ DAD S + + +AG LMP +A+ AP Sbjct: 253 WSPDYPGQSGHIHLSLNHADSGESAFFDADQPHGMSDIQRHFVAGQQKLMPEFLAMFAPT 312 Query: 329 VNSYRRFQPGMYVPTQASWGHNNRTVALRIPCGDRHNHRVEYRVAGADANPYLVMAAIFA 388 VNSY R PG + PT A+WG NRT ALR+ G + RVEYR+ ADANPYL +AA Sbjct: 313 VNSYTRLIPGFWAPTDATWGVENRTTALRVIPGSAKSQRVEYRLGSADANPYLALAAAIG 372 Query: 389 GILHGLDNPLPLQEEVEGNGLEQEGLPFPIRQ--SDALWEFMQ----NDHLRERLGERFC 442 L+G+++ L E V GN E L P Q S LWE Q +D R G+ F Sbjct: 373 SGLYGIEHQLEPDEMVTGNSYE---LAHPEHQALSRTLWEAAQRLKASDAARSLFGDAFV 429 Query: 443 HVYHACKNDELLQFERLITETEIE 466 + A + E QF R IT+ E++ Sbjct: 430 EHFAATREWEERQFRRHITDWELD 453 Lambda K H 0.319 0.136 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: 531 Number of extensions: 23 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: 472 Length of database: 459 Length adjustment: 33 Effective length of query: 439 Effective length of database: 426 Effective search space: 187014 Effective search space used: 187014 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 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