Align glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41) (characterized)
to candidate WP_011842417.1 RSPH17029_RS17760 glutamate-5-semialdehyde dehydrogenase
Query= BRENDA::Q9Z110 (795 letters) >NCBI__GCF_000015985.1:WP_011842417.1 Length = 420 Score = 268 bits (686), Expect = 3e-76 Identities = 158/404 (39%), Positives = 241/404 (59%), Gaps = 7/404 (1%) Query: 367 GEMARSGGRMLATLEPEQRAEIINHLADLLTDQREEILLANKKDLE-EAEGRLASPLLKR 425 G AR+ LA EP ++ E +N A+ + + +EIL AN +DL AE L ++ R Sbjct: 14 GVRARAAAAELAFAEPSRKEEALNAAAEAMLARSDEILEANGRDLAFGAEKGLTPAMMDR 73 Query: 426 LSLSTSKLNSLAIGLRQIAASSQESVGRVLRRTRIAKNLELEQVTVPIGVLLVIFESRPD 485 L L ++++ + GLR +A + VG+V+ L + +V P+GV+ VI+ESRP+ Sbjct: 74 LKLDAARIDGIVEGLRAVAGQP-DPVGQVIAEWDRPSGLHIRRVRTPLGVVGVIYESRPN 132 Query: 486 CLPQVAALAIASGNGLLLKGGKEAAHSNRILHLLTQEALSIHGVK-EAIQLVNTREE--V 542 AL + SGN ++L+GG E+ HS+ +H Q+ L G+ +AIQ V TR+ V Sbjct: 133 VTADAGALCLKSGNAVILRGGSESFHSSGAIHAALQDGLRQAGLPVDAIQRVPTRDRAAV 192 Query: 543 EDLCRLDKIIDLIIPRGSSQLVRDIQKAAKGIPVMGHSEGICHMYVDSEASVDKVTRLVR 602 ++ R+ + ID+I+PRG LV +Q A+ +PV H EGICH+Y D +A ++K R+V Sbjct: 193 AEMLRMVEHIDVIVPRGGKGLVGLVQAEAR-VPVFAHLEGICHVYADGDADLEKARRVVL 251 Query: 603 DSKCEYPAACNALETLLIHRDLLRTPLFDQIIDMLRVEQVKIHAGPKFASYLTFSPSEVK 662 ++K C + E LLI R L I D+L+ V++ A + A P++ + Sbjct: 252 NAKTRRTGICGSAECLLIDRAFLAKHGPVLIEDLLKAG-VEVRAEGELAQVPGTVPAQPE 310 Query: 663 SLRTEYGDLEVCIEVVDSVQEAIDHIHKYGSSHTDVIVTENEKTAEFFLQHVDSACVFWN 722 E+ D+ + +VVD V EAI HI +YGSSHT+ I+TEN+ TAE F + +DSA + N Sbjct: 311 DFGREFLDMIIAAKVVDGVDEAIAHIRRYGSSHTESILTENDATAERFFRRLDSAILMRN 370 Query: 723 ASTRFSDGYRFGLGAEVGISTSRIHARGPVGLEGLLTTKWLLRG 766 AST+F+DG FG+GAE+GI+T ++HARGPVG E L + K+L+ G Sbjct: 371 ASTQFADGGEFGMGAEIGIATGKMHARGPVGAEQLTSFKYLVTG 414 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: 747 Number of extensions: 36 Number of successful extensions: 5 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: 420 Length adjustment: 36 Effective length of query: 759 Effective length of database: 384 Effective search space: 291456 Effective search space used: 291456 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 16 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