Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF543 PGA1_c05550 glutamine synthase-like protein
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__Phaeo:GFF543 Length = 483 Score = 183 bits (465), Expect = 9e-51 Identities = 137/448 (30%), Positives = 208/448 (46%), Gaps = 28/448 (6%) Query: 12 RVTEIEAIIPDMAGIARGKIIP----RSKFESGESMRLPQAVMIQT--------VTGDYP 59 RV + + D GI RGK + RS FE G + +P ++++ V + P Sbjct: 35 RVETVRVLFADQHGILRGKTLVAAGLRSLFEQG--IAVPSTLLLKDTAHRTVFPVWSENP 92 Query: 60 EDGTLTGVTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLE 119 E+ D++ VP T R++PW+ H H DG V VL R + Sbjct: 93 EEVVTPMQGASDVLLVPRPETFRVLPWSPHSAWIFCHVAFH-DGATVPFGSAHVLERAVA 151 Query: 120 LYKAKGWKPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRP-ET-----GRQAYSIEAVNE 173 +G + V+ E+EF + + DP L G G P ET G Q + E Sbjct: 152 TLAEQGLQTVVGLEVEFQIFE-RVDPALG-HAQQGMPGAPIETRNLIQGYQYLTETRYAE 209 Query: 174 FDPLFEDIYEYCEVQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALR 233 + + + + + + L V T+ E+G +Q E F DP+ AD++ +F+ +E Sbjct: 210 AEGILDALRRHAQALGLPVRTVEIEMGPSQFEFTFDPADPMTQADAMVMFRTMAKEVCAA 269 Query: 234 HKMYATFMAKPMEGEP-GSAMHMHQSLVDEETGHNLFTGPD--GKPTSLFTSYIAGLQKY 290 + ++A+FMAKP + + H+HQSL+D +G NLF P+ G+ T+ + +IAGL + Sbjct: 270 NGLHASFMAKPRQDHAMANGWHIHQSLIDTVSGRNLFM-PEVAGELTAEASGWIAGLLAH 328 Query: 291 TPALMPIFAPYINSYRRLSRFMAAPINVAWGYDNRTVGFR-IPHSGPAARRIENRIPGVD 349 A + AP +NSY+R + AP V WG DNR R + G R+ENR P Sbjct: 329 AEAASILVAPTVNSYKRYLPYQLAPNRVQWGEDNRGAMLRGLMRPGDPTSRVENRAPDST 388 Query: 350 CNPYLAIAATLAAGYLGMTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVL 409 NPY A+AA + AG GM A P S + +LPR+L + L + E L Sbjct: 389 ANPYFALAAQIIAGSEGMMAGRRAPAPTASPYSDDAEKLPRSLGQALQAFSSSELFRSAL 448 Query: 410 GEKFVKAYLALKETEYEAFFRVISSWER 437 GE V LKE E+ + +S WE+ Sbjct: 449 GEDVVDYLTHLKEVEWARYLDTVSEWEQ 476 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: 551 Number of extensions: 29 Number of successful extensions: 6 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: 444 Length of database: 483 Length adjustment: 33 Effective length of query: 411 Effective length of database: 450 Effective search space: 184950 Effective search space used: 184950 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 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