Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_011840207.1 RSPH17029_RS00810 aldehyde dehydrogenase family protein
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_000015985.1:WP_011840207.1 Length = 486 Score = 296 bits (759), Expect = 8e-85 Identities = 170/476 (35%), Positives = 262/476 (55%), Gaps = 19/476 (3%) Query: 10 RQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTA 69 R+ YING W + +V +P+T E + A+T A+ AA A W A Sbjct: 4 RRDFYINGGWTAPAKARDCEVIDPSTEEACAVISLGDQADTDAAVAAAKAAFEGWAATPP 63 Query: 70 KERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIA-----YAASFIEWFAE-EA 123 ER ++ ++++A+ ++ E G P+ A+ A + +F++ F E E Sbjct: 64 AERLRLVKGILAQYEARKEEMAQAISLEMGAPIDLARNSQAPCLPWHLTNFLKAFEEIEW 123 Query: 124 KRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPAS 183 R G H P+ R+ + +PIGV ITPWN+P +T K PAL AGCT VLKP+ Sbjct: 124 VRPLGP----HAPNDRIAL--EPIGVVGLITPWNWPMNQVTLKVIPALLAGCTCVLKPSE 177 Query: 184 QTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLME 243 + P S+L E H AG+PAGV ++V G VG +L+ + V +SFTGST GR + + Sbjct: 178 EAPLSSLLFAEFVHDAGLPAGVFNLVNGDGAGVGTQLSSHPDVEMISFTGSTRAGRAISK 237 Query: 244 ECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYD 303 A+ +K+V+LELGG ++F DAD ++AVE + + N+GQ+C R+ V+ YD Sbjct: 238 AAAESLKRVTLELGGKGANLIFADAD-ERAVERGVKHCFNNSGQSCNAPTRMLVERPFYD 296 Query: 304 AFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGG----- 358 E A AK ++ + EEG GP+++ + ++Q +I+ + +GA++++GG Sbjct: 297 RAVEIAAEVAAKTRVASAHEEGPHIGPVVNKRQFEQIQSYIQKGIDEGARLVAGGLGRPD 356 Query: 359 KLIEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYA 418 L G F PT+ DV + +EE FGP+ + F+ E E + ++NDT +GL +Y + Sbjct: 357 GLNRGFFVRPTVFADVTPGMTIEREEIFGPVLSILPFETEEEAVRIANDTPYGLTNYVQS 416 Query: 419 RDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 D +R R+A L GMV +N G APFGG+KASG REG +GIE++LE+K Sbjct: 417 EDGARRNRLARRLRSGMVEMN-GKSRGAGAPFGGVKASGRAREGGVWGIEEFLEVK 471 Lambda K H 0.317 0.134 0.384 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: 545 Number of extensions: 27 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: 480 Length of database: 486 Length adjustment: 34 Effective length of query: 446 Effective length of database: 452 Effective search space: 201592 Effective search space used: 201592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 10 2024. 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