Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_057507768.1 ABB28_RS05980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_001431535.1:WP_057507768.1 Length = 454 Score = 232 bits (592), Expect = 2e-65 Identities = 148/464 (31%), Positives = 237/464 (51%), Gaps = 18/464 (3%) Query: 36 TFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLME 95 T E V+P T + I++ + AA G F WS +S +R AVL + + Sbjct: 2 TVEIVNPTTGRVDYRHELLDKAGIEQRLQAAAGAFPA--WSATSLQERAAVLRAIGAQLR 59 Query: 96 AHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAE-AIDKVYGEVATTSSHELAMIV 154 +++ T + GK ++ ++ A A +YA+ A D + ++ T + + + Sbjct: 60 ERKDDIQGAMTREMGK-LKVEALAEVEKCAAACEYYADHAADYLKPQLIDTEAQR-SYVR 117 Query: 155 REPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPD 214 EP+G + A++PWNFP+ L PA AGN +LK + P A + + + GLPD Sbjct: 118 YEPIGCVFAVMPWNFPIWQVFRFLAPAFMAGNVALLKHASNVPQCADLINEVVRAGGLPD 177 Query: 215 GVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSAN 274 GV +V+ +A L R + A+ TGS R G+ + +AGD +K+ +E GG A Sbjct: 178 GVFDVLHIDNDQAADVL-RDRRVKAVTLTGSERAGRSIAANAGDQ-LKKCVMELGGSDAF 235 Query: 275 IVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHP 334 +V D DL +A A F N GQ CIA R ++ E++AD F A + G P Sbjct: 236 VVLDDA-DLDKAIDAAVKSRFDNSGQTCIAAKRFIVVEAVADAFTERFVAAAGERRYGDP 294 Query: 335 LDPATTMGTLIDCAHADSVHSFIREGESKGQLLL------DGRNAGLAAAIGPTIFVDVD 388 D TT+ + D +H ++ +KG +L DG +AG A T+ V Sbjct: 295 ADARTTLAPMARADLRDELHKQVQASVAKGARVLAGGEPVDGSHAGYPA----TVLDQVG 350 Query: 389 PNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGS 448 P EE+FGPV V R E +AL++AND+++GLG +VWT D +R +++++ G+ Sbjct: 351 PGMPAYDEELFGPVAAVIRVKDEAEALKVANDTRFGLGGSVWTTDAARGEAFAQQMECGA 410 Query: 449 VFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWIS 492 FVN+ D+ +PFGG K+SG GR+ + H + +F +KTI+++ Sbjct: 411 AFVNSIVKSDVRLPFGGSKESGFGRELAEHGIHEFMNIKTIYVA 454 Lambda K H 0.317 0.133 0.389 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: 489 Number of extensions: 24 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: 495 Length of database: 454 Length adjustment: 33 Effective length of query: 462 Effective length of database: 421 Effective search space: 194502 Effective search space used: 194502 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