Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate GFF1533 PGA1_c15520 gamma-glutamyl phosphate reductase ProA
Query= BRENDA::Q9Z110 (795 letters) >FitnessBrowser__Phaeo:GFF1533 Length = 421 Score = 260 bits (664), Expect = 1e-73 Identities = 152/404 (37%), Positives = 230/404 (56%), Gaps = 7/404 (1%) Query: 367 GEMARSGGRMLATLEPEQRAEIINHLADLLTDQREEILLANKKDLEEAEGRLASP-LLKR 425 G+ A+ LAT E++A+ +N AD + D R EIL AN KDL+ + SP ++ R Sbjct: 15 GKRAKQAAAKLATATAERKADALNAAADAVWDARAEILGANAKDLDFGRNKGLSPAMMDR 74 Query: 426 LSLSTSKLNSLAIGLRQIAASSQESVGRVLRRTRIAKNLELEQVTVPIGVLLVIFESRPD 485 L+L +++ + GLR +AA + VG VL L++++V P+GV+ VI+ESRP+ Sbjct: 75 LALDEDRISGIVAGLRAVAAQP-DPVGEVLAEWSQPSGLDIQRVRTPLGVIGVIYESRPN 133 Query: 486 CLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGVKE-AIQLVNTREE--V 542 AL + SGN ++L+GG E+ +S++ +H L + E AIQLV TR+ V Sbjct: 134 VTADAGALCLKSGNAVILRGGSESFYSSQAIHGCLAAGLRAADLPEDAIQLVPTRDRAAV 193 Query: 543 EDLCRLDKIIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVTRLVR 602 ++L + +D+I+PRG LV +Q+ A+ +PV H EGI H+Y+D +A K +V Sbjct: 194 QELLTMTDTVDVIVPRGGKGLVGLVQREAR-VPVFAHLEGIVHIYLDKDADPQKALEIVL 252 Query: 603 DSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQVKIHAGPKFASYLTFSPSEVK 662 ++K C A E LLIHRD+ T + ++ L V+I A + + Sbjct: 253 NAKTRRTGICGAAECLLIHRDIAET-IGRDVLTALATAGVEIRAEAGLPGPDGMTAATSA 311 Query: 663 SLRTEYGDLEVCIEVVDSVQEAIDHIHKYGSSHTDVIVTENEKTAEFFLQHVDSACVFWN 722 EY D + + VD + AIDHI + S HTD I+TEN+ F +DSA + N Sbjct: 312 DWGCEYLDAIIAAKQVDDIDAAIDHIRTHHSQHTDCIITENDSAVAQFFAELDSAILMHN 371 Query: 723 ASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRG 766 AST+F+DG FG+GAE+GI+T ++HARGPVG L + K+L+RG Sbjct: 372 ASTQFADGGEFGMGAEIGIATGKMHARGPVGAAQLTSFKYLVRG 415 Lambda K H 0.319 0.134 0.383 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: 666 Number of extensions: 35 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: 795 Length of database: 421 Length adjustment: 36 Effective length of query: 759 Effective length of database: 385 Effective search space: 292215 Effective search space used: 292215 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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