Align succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized)
to candidate AZOBR_RS32475 AZOBR_RS32475 aldehyde Dehydrogenase
Query= CharProtDB::CH_007085 (453 letters) >FitnessBrowser__azobra:AZOBR_RS32475 Length = 475 Score = 296 bits (758), Expect = 1e-84 Identities = 172/458 (37%), Positives = 267/458 (58%), Gaps = 9/458 (1%) Query: 2 SNEVSIKELIEKAKVAQKKLEAYSQEQVDVLVKALGKVVYD--NAEMFAKEAVEETEMGV 59 +++ +I L+ +A+ AQ+ +QE+VD V AL +Y+ A A+ AV +T +G Sbjct: 13 ADQEAIAALVARARTAQRAFADATQERVDDAVAALAWAIYEPGRARALAELAVADTGLGN 72 Query: 60 YEDKVAKCHLKSGAIWNHIKDKKTVGIIKEEPERALVYVAKPKGVVAATTPITNPVVTPM 119 DK+ K K+ + +TVG+I+E+ + +V +AKP GVV A TP TNP TP+ Sbjct: 73 VADKIVKNQRKTFGTLRDLMRVRTVGVIEEDTAKGIVKIAKPLGVVGAVTPSTNPAATPV 132 Query: 120 CNAMAAIKGRNTIIVAPHPKAKKVSAHTVELMNAELKKLGAPENIIQIVEAP-SREAAKE 178 AM A+KGRN II+AP P + TVELM AEL ++GAPE+++Q++ P ++ + Sbjct: 133 NKAMMAVKGRNAIIIAPSPMGSAATGRTVELMRAELARIGAPEDLVQMIPTPITKGLTQA 192 Query: 179 LMESADVVIATGGAGRVKAAYSSGRPAYGVGPGNSQVIVDKGYDYNKAAQDIITGRKYDN 238 LME+ D+V+ TG V+ AYSSG PA GVG GN VIVD+ D +AA+ I + +DN Sbjct: 193 LMEAVDLVVVTGSQDNVRRAYSSGTPAIGVGAGNVPVIVDESADLAEAARKIGASKTFDN 252 Query: 239 GIICSSEQSVIAPAEDYDKVIAAFVENGAFYVEDEETVEKFRSTLFKDGKINSKIIGKSV 298 CSSE +++ YD IAA E GA EE E+ +S L+++GK+N K+I K Sbjct: 253 STSCSSENALVVLDSVYDATIAALEEAGAHLCTPEER-ERVQSRLWENGKLNRKLIAKDP 311 Query: 299 QIIADLAGVKVPEG--TKVIVLKGKGAGEKDVLCKEKMCPVLVALKYDTFEEAVEIAMAN 356 I+A+ A P+ + +++ G G+ EK+ VL + F+ AV+ Sbjct: 312 AILAE-AFELAPKAREARFFLVEETGVGKAHPFSGEKLSLVLAVYRVPDFDAAVDQVRKI 370 Query: 357 YMYEGAGHTAGIHSDNDENIRYAGTVLPISRLVVNQPATTA-GGSFNNGFNPTTTLGCGS 415 ++G GH+ GIH+ ++ + + L + R++VN T GG F++G N T ++GCGS Sbjct: 371 LDHQGRGHSCGIHTRDEAHAKRLADELDVVRVLVNFAHTFGNGGGFDSGLNFTLSMGCGS 430 Query: 416 WGRNSISENLTYEHLINVSRIGYFNKEAKVPSYEEIWG 453 W +NSISENL+++H +N++ + E K PS E ++G Sbjct: 431 WQKNSISENLSWKHFVNITHLVRPIPEDK-PSEEALFG 467 Lambda K H 0.313 0.131 0.368 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: 568 Number of extensions: 27 Number of successful extensions: 6 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: 453 Length of database: 475 Length adjustment: 33 Effective length of query: 420 Effective length of database: 442 Effective search space: 185640 Effective search space used: 185640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 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