Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate AO353_29295 AO353_29295 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29295 Length = 496 Score = 542 bits (1397), Expect = e-159 Identities = 275/489 (56%), Positives = 345/489 (70%), Gaps = 4/489 (0%) Query: 9 WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68 W+ SL IE R FI+G Y +A +TFE V PV LA +A D + A+ AR Sbjct: 8 WEQHFQSLTIEGRAFIDGHYCSALSRDTFECVSPVDGRFLANVASTDEADANAAVQVARR 67 Query: 69 VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128 F+ G W+ +PA+RK +L + ADL+ A+ EELALLETLD GKPI S+ DIP A AI Sbjct: 68 AFDSGVWAKLAPAERKRILIRFADLILANQEELALLETLDMGKPISDSMAIDIPATANAI 127 Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188 RW AEAIDK+Y EVA T +L ++ REP GV+AAIVPWNFPL++ WK PALAAGNS Sbjct: 128 RWSAEAIDKIYDEVAATPHDQLGLVTREPSGVVAAIVPWNFPLIMASWKFAPALAAGNSF 187 Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248 ILKPSEKSPL+AIR+A LA +AG+P GV NV+ GFGH G+AL+ H D+D +AFTGST Sbjct: 188 ILKPSEKSPLTAIRIAQLALDAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAFTGSTAI 247 Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308 KQLL AG SNMKRVWLEAGGKS N+VFAD PDL+ AA+A A+ I +NQG+VC AG+RL Sbjct: 248 AKQLLIYAGQSNMKRVWLEAGGKSPNVVFADAPDLRAAATAAASAIAFNQGEVCTAGSRL 307 Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368 L+E SI ++F+ LL + Q W+PGH LDP TT+G ++D D+V +I G+ +G L+ Sbjct: 308 LVERSIREQFIPLLVEALQAWKPGHALDPETTVGAVVDQRQLDNVLRYISIGKEQGAQLI 367 Query: 369 DGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424 G N L G P IF V +++REEIFGPVL + F + E+AL +ANDS +G Sbjct: 368 AGGNRALEDTGGLYVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALAIANDSIFG 427 Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFT 484 L A VWT +LS+AH +R L+AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHA +K+T Sbjct: 428 LAAGVWTSNLSKAHTFARGLRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYT 487 Query: 485 ELKTIWISL 493 ELK WI L Sbjct: 488 ELKATWIKL 496 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: 616 Number of extensions: 15 Number of successful extensions: 2 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: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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