Align Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_495 (480 letters) >NCBI__GCF_001431535.1:WP_057507768.1 Length = 454 Score = 273 bits (697), Expect = 1e-77 Identities = 159/453 (35%), Positives = 247/453 (54%), Gaps = 10/453 (2%) Query: 27 TIKVNNPATGEILGTVPKMGAAETRRAIEAADKALPAWRALTAKERATKLRRWYELIIEN 86 T+++ NP TG + + A + ++AA A PAW A + +ERA LR + E Sbjct: 2 TVEIVNPTTGRVDYRHELLDKAGIEQRLQAAAGAFPAWSATSLQERAAVLRAIGAQLRER 61 Query: 87 QDDLARLMTLEQGKPLAEAKGEIVYAASFIEWFAEEAKRIYGDVIPGHQPD---KRLIVI 143 +DD+ MT E GK EA E+ A+ E++A+ A D + D +R V Sbjct: 62 KDDIQGAMTREMGKLKVEALAEVEKCAAACEYYADHA----ADYLKPQLIDTEAQRSYVR 117 Query: 144 KQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSAFALAELAQRAGIPA 203 +PIG A+ PWNFP + R PA AG +LK AS P A + E+ + G+P Sbjct: 118 YEPIGCVFAVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPD 177 Query: 204 GVFSVVSGSAGDIGSELTSNPIVRKLSFTGSTEIGRQLMSECAKDIKKVSLELGGNAPFI 263 GVF V+ D +++ + V+ ++ TGS GR + + +KK +ELGG+ F+ Sbjct: 178 GVFDVLHID-NDQAADVLRDRRVKAVTLTGSERAGRSIAANAGDQLKKCVMELGGSDAFV 236 Query: 264 VFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDGVYDAFAEKLKVAVAKLKIGNGLE 323 V DDADLDKA++ A+ S++ N+GQTC+ A R + + V DAF E+ A + + G+ + Sbjct: 237 VLDDADLDKAIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDPAD 296 Query: 324 AGTTTGPLIDEKAVAKVQEHIADALSKGATVLAGGKPMEGNF--FEPTILTNVPNNAAVA 381 A TT P+ ++ + + +++KGA VLAGG+P++G+ + T+L V Sbjct: 297 ARTTLAPMARADLRDELHKQVQASVAKGARVLAGGEPVDGSHAGYPATVLDQVGPGMPAY 356 Query: 382 KEETFGPLAPLFRFKDEADVIAMSNDTEFGLASYFYARDLGRVFRVAEALEYGMVGVNTG 441 EE FGP+A + R KDEA+ + ++NDT FGL + D R A+ +E G VN+ Sbjct: 357 DEELFGPVAAVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGAAFVNSI 416 Query: 442 LISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 + S+ PFGG K SG GRE +++GI +++ IK Sbjct: 417 VKSDVRLPFGGSKESGFGRELAEHGIHEFMNIK 449 Lambda K H 0.317 0.135 0.390 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: 510 Number of extensions: 21 Number of successful extensions: 4 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: 454 Length adjustment: 33 Effective length of query: 447 Effective length of database: 421 Effective search space: 188187 Effective search space used: 188187 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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