Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate 3608063 Dshi_1469 gamma-glutamyl phosphate reductase (RefSeq)
Query= BRENDA::Q941T1 (735 letters) >FitnessBrowser__Dino:3608063 Length = 421 Score = 269 bits (688), Expect = 2e-76 Identities = 146/416 (35%), Positives = 229/416 (55%), Gaps = 14/416 (3%) Query: 312 ATAREMAVAARDCSRHLQKLSSEERKKILLDIADALEANEDLITSENQADLDLAQDIGYD 371 A E+ AA+ + L +++R + L ADA+ A D I + N DLD +D G Sbjct: 9 ALMAEIGTAAKAAAAELAFAPADQRAQALTAAADAVWARRDEIIAANARDLDYGRDKGLS 68 Query: 372 KSLVARMTIKPGKIKSLAGSIREIADMEDPISHTLKRTEVAKDLVFEKTYCPLGVLLIIF 431 +++ R+ + +I+ + +R +A +DP+ L + L + PLGV+ +I+ Sbjct: 69 PAMMDRLALDEARIQGIVDGLRAVAAQDDPVGAVLSEWDRPTGLHIRRVRTPLGVIGVIY 128 Query: 432 ESRPDALVQIASLAIRSGNGLLLKGGKEAMRSNTILHKVITGAIPDV-VGKKLIGLVKNK 490 ESRP+ +L ++SGN ++L+GG E+ S++++H + + + + I LV + Sbjct: 129 ESRPNVTADAGALCLKSGNAVILRGGSESFHSSSLIHACLRDGLRAADLPETAIQLVPTR 188 Query: 491 DEIA--DLLKLDDVIDLVIPRGSNKLVSQIKAATKIPVLGHADGICHVYIDKSADMDMAK 548 D A ++L + D ID++IPRG LV +++A ++PV H +GICH+Y+D AD D Sbjct: 189 DRAAVGEMLTMTDTIDVIIPRGGKGLVGRVQAEARVPVFAHLEGICHIYVDADADPDKTA 248 Query: 549 RIVLDAKVDYPAACNAMETLLVHKDLNRTEGLDDLLVELEKEGVVIYGGPVAHDTLKL-- 606 R++L+AK C A E LLV + G + +L GV + A DTL+ Sbjct: 249 RVILNAKTRRTGICGAAECLLVDRAWYDRNGAT-FIADLIAAGVEVR----ADDTLQAIP 303 Query: 607 ----PKVDSFHHEYNSMACTLEFVDDVQSAIDHINRYGSAHTDCIITTDGKAAETFLQQV 662 K D F E+ M VD V AI HI RYGS HTDCI+T + A F Q++ Sbjct: 304 GTVPAKADDFGREFLDMIIAARVVDGVDGAIAHIRRYGSQHTDCILTENDATAARFFQRL 363 Query: 663 DSAAVFHNASTRFCDGARFGLGAEVGISTGRIHARGPVGVDGLLTTRCILRGSGQV 718 DSA + NAST+F DG FG+GAE+GI+TG++HARGPVG + L + + ++ G G + Sbjct: 364 DSAILMRNASTQFADGGEFGMGAEIGIATGKMHARGPVGAEQLTSFKYLVEGDGTI 419 Lambda K H 0.318 0.136 0.385 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: 704 Number of extensions: 31 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: 735 Length of database: 421 Length adjustment: 36 Effective length of query: 699 Effective length of database: 385 Effective search space: 269115 Effective search space used: 269115 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 (21.7 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