Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_057509241.1 ABB28_RS14190 type I glutamate--ammonia ligase
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >NCBI__GCF_001431535.1:WP_057509241.1 Length = 469 Score = 134 bits (338), Expect = 5e-36 Identities = 127/469 (27%), Positives = 200/469 (42%), Gaps = 58/469 (12%) Query: 1 MHDIDDFLKKNRVTEIEAIIPDMAGIARG-----KIIPRSKFESGESMRLPQAVMIQTVT 55 + +++ +K N++ ++ DM GI + II S FE G+ Sbjct: 3 VENVEKLVKDNQIEFVDLRFVDMRGIEQHVTFPVSIIEASLFEEGKMF------------ 50 Query: 56 GDYPEDGTLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGT---PVAISPRR 112 D G+ + DMV +PD S+ + P+ DPT ++ C D P PR Sbjct: 51 -DGSSIAGWKGINESDMVLLPDPSSAYVDPFYADPT--IVISCDILDPATMQPYGRCPRG 107 Query: 113 VLRRVLELYKAKG--WKPVIAPELEFYLVDM--------NKDPDLPLQPPIGRTG----- 157 + +R K+ G + PE EF++ D N + + TG Sbjct: 108 IAKRAEAFLKSSGIAEQAFFGPEPEFFIFDSVRFANDMGNTFFKVDSEEAAWNTGAKYDG 167 Query: 158 -----RPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTLIHEVG-AAQMEINFMHG 211 RP + + + L ++ + E +EV+ HEV A Q EI Sbjct: 168 ANSGYRPGVKGGYFPVPPTDSLHDLRAEMCKTLEQVGIEVEVQHHEVATAGQCEIGTKFS 227 Query: 212 DPLKLADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHMHQSLVDEETGHNLFTG 271 ++ AD + K ++ A R+ ATFM KP+ G+ GS MH+HQSL + G NLF+G Sbjct: 228 TLVQKADELLRMKYVIKNVAHRNGKTATFMPKPIVGDNGSGMHVHQSL--SKGGTNLFSG 285 Query: 272 PD-GKPTSLFTSYIAGLQKYTPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFR 330 G + L YI G+ K+ A+ NSY+RL AP+ +A+ NR+ R Sbjct: 286 DGYGGLSQLALWYIGGIFKHAKAINAFANAGTNSYKRLVPGFEAPVMLAYSARNRSASCR 345 Query: 331 IPH-SGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELP---- 385 IP + P ARRIE R P + YL + AG G+ +++ P D Y+LP Sbjct: 346 IPFVTNPKARRIEMRFPDPIQSGYLTFTVLMMAGLDGIKNQIDPGAPSDKDLYDLPPEEE 405 Query: 386 ---YQLPRNLEEGLTLMGACEPIAE---VLGEKFVKAYLALKETEYEAF 428 Q+ +L++ L + + V+ + F+ Y+ALK E F Sbjct: 406 KLIPQVCSSLDQALEALDKDREFLKAGGVMDDDFIDGYIALKMQEVTKF 454 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: 545 Number of extensions: 36 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 444 Length of database: 469 Length adjustment: 33 Effective length of query: 411 Effective length of database: 436 Effective search space: 179196 Effective search space used: 179196 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