Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate Pf6N2E2_5686 glutamine synthetase family protein
Query= reanno::BFirm:BPHYT_RS23160 (444 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5686 Length = 447 Score = 344 bits (883), Expect = 3e-99 Identities = 179/434 (41%), Positives = 250/434 (57%), Gaps = 12/434 (2%) Query: 13 VTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLTGVTDPDM 72 + EIE + PD+ G+ RGK++ F G ++L + V++Q + G YP G D D+ Sbjct: 16 IDEIECVTPDLNGVPRGKVMTAEGFLEGRRLQLARGVLLQCIMGGYPPS-RFYGSDDGDL 74 Query: 73 VCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKGWKPVIAP 132 V D I +PW+ P A I D G +S R L+ V+ Y A G PV+A Sbjct: 75 ALVADPKQIHRLPWSQQPRALAICDADELTGESSRLSTRGQLKAVVARYAALGLAPVVAT 134 Query: 133 ELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEV 192 ELEF++ N DP P QPP+G GR E G A+S+ + N P F ++Y L Sbjct: 135 ELEFFVFAPNPDPTQPFQPPMGLDGRREDGHSAFSVSSNNGLRPFFSEVYACMAALGLPR 194 Query: 193 DTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSA 252 DT +HE+G +Q EIN +HGDPL LAD FLFK ++E AL+H + MAKP+ PGS+ Sbjct: 195 DTFMHEMGVSQFEINLLHGDPLLLADQTFLFKHLLKEVALKHGLTVVCMAKPLAHTPGSS 254 Query: 253 MHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYINSYRRLSRFM 312 MH+HQS+V+E +G N+F+ G+PT+ F +I G Q +FAP +NSY+RL Sbjct: 255 MHIHQSVVEEGSGRNVFSDEAGEPTAAFRHFIGGQQACLADFTALFAPNVNSYQRLCHPF 314 Query: 313 AAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLE 372 A+P N W +DNR+ G RIP S P ARR+ENR+PG D NPYLAIAA+LAAG G+ +LE Sbjct: 315 ASPNNACWSHDNRSAGLRIPASSPVARRVENRLPGADANPYLAIAASLAAGLYGIEHRLE 374 Query: 373 ATEPLLSDGYELPYQLPRNLEEGLTLMGACEPI------AEVLGEKFVKAYLALKETEYE 426 + + + +++P NL TL A E + E+ G +F++ Y+A K E Sbjct: 375 PSAAIQGE-----FEVPDNLSLPCTLHAALERLKRSHLAKELFGTEFIEGYIASKTLELT 429 Query: 427 AFFRVISSWERRHL 440 +FF I+ WERR L Sbjct: 430 SFFDEITPWERRVL 443 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: 592 Number of extensions: 23 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: 444 Length of database: 447 Length adjustment: 32 Effective length of query: 412 Effective length of database: 415 Effective search space: 170980 Effective search space used: 170980 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