Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_073948994.1 RH94_RS20650 aldehyde dehydrogenase family protein
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_001906585.1:WP_073948994.1 Length = 462 Score = 307 bits (787), Expect = 4e-88 Identities = 181/472 (38%), Positives = 260/472 (55%), Gaps = 28/472 (5%) Query: 14 YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73 YI+G W A I+V NPA +VI TVP + A+ AA ALP W A ER+ Sbjct: 8 YIDGAWRPAAGRDAIEVVNPADEQVIATVPAGTAEDVDAAVRAARAALPGWAATPPAERA 67 Query: 74 AKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG-----EIAYAASFIEWFAEEA-KRIY 127 A+L ++++ +D++A +T E G PLA ++ IA A S+ + A A + Sbjct: 68 ARLTALRDVLVARKDEIAETVTAELGSPLAFSQAVHAGVPIAVAGSYADLAATYAFEEKV 127 Query: 128 GDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPY 187 G++ H+P +GV AITPWN+P I KA PALAAGCT+VLKPA TP Sbjct: 128 GNSTVHHEP----------VGVVGAITPWNYPLHQIVAKAAPALAAGCTIVLKPAEDTPL 177 Query: 188 SALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAK 247 +A E AH AGIPAGVL++VTG G L + V +SFTGST +GR++ Sbjct: 178 TAQLFAEAAHEAGIPAGVLNLVTGLGPVAGQALAEHPDVDLVSFTGSTAVGRRIGATAGA 237 Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAE 307 +K+V+LELGG + ++ ADL +AV + + N+GQTC R+ V YD E Sbjct: 238 AVKRVALELGGKSANVILPSADLARAVNVGVANVMSNSGQTCSAWTRMLVHRDQYDEAVE 297 Query: 308 KLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGG---KLIEGN 364 A A AK G GP+++ K A+V+ +IE +++GA++++GG +G Sbjct: 298 LAATAAAKY--------GDRIGPVVNAKQRARVRGYIEKGIAEGARLVAGGPEAPCEKGY 349 Query: 365 FFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRV 424 F PT+ DV VA+EE FGP+ + R+ DE + + ++N T +GLA +A D + Sbjct: 350 FVSPTVFADVTPDMTVAQEEIFGPVLSILRYDDEDDALRIANGTVYGLAGAVWAADETEA 409 Query: 425 FRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476 A ++ G V IN G N +APFGG K SG+GRE +G+ +YL+ K L Sbjct: 410 VAFARRMDTGQVDINGGRF-NPLAPFGGYKQSGVGRELGAHGLTEYLQTKSL 460 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: 548 Number of extensions: 14 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: 462 Length adjustment: 33 Effective length of query: 447 Effective length of database: 429 Effective search space: 191763 Effective search space used: 191763 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: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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