Align succinate-semialdehyde dehydrogenase [NAD(P)+] (EC 1.2.1.16) (characterized)
to candidate GFF3650 PGA1_262p00540 succinate-semialdehyde dehdyrogenase GabD
Query= BRENDA::Q8ZPI3 (462 letters) >FitnessBrowser__Phaeo:GFF3650 Length = 459 Score = 386 bits (991), Expect = e-112 Identities = 206/449 (45%), Positives = 285/449 (63%), Gaps = 2/449 (0%) Query: 11 SVNPATGQTLAAMPWANAQEIEHALSLAASGFKKWKMTSVAQRAQTLRDIGQALRAHAEE 70 +VNP TG+TL + + +E A+ + F W++TSV RA T++ IG ALR +E Sbjct: 7 TVNPTTGKTLDTYNVLSGKALEDAVQRCHNAFLDWRLTSVEDRANTIKAIGAALRDRKDE 66 Query: 71 MAQCITREMGKPIKQARAEVTKSAALCDWYAEHGPAMLNPEPTLVEN-QQAVIEYRPLGV 129 +A+ +T+EMGK +KQ+ E+ AA+CD+ A PA PE +E ++ I Y P+GV Sbjct: 67 LAELMTKEMGKLLKQSHQEIDLCAAICDYSAAEAPAAFAPEERDIEGGEKGHIFYSPIGV 126 Query: 130 ILAIMPWNFPLWQVLRGAVPILLAGNSYLLKHAPNVTGCAQMIARILAEAGTPAGVYGWV 189 + I PWNFP +QV+R ++ L+AGN LLKHA NVTG QM+ I AG P G++ + Sbjct: 127 VYGIQPWNFPAYQVVRYSIASLIAGNGVLLKHASNVTGSGQMLQEIYEAAGLPKGLFQAL 186 Query: 190 NANNEGVSQMINDPRIAAVTVTGSVRAGAAIGAQAGAALKKCVLELGGSDPFIVLNDADL 249 +++ +I+ + VT+TGS AG +GA+A A+KK VLELG +D +IVL DAD+ Sbjct: 187 VISHDQSDTLISHDLVRGVTLTGSDGAGRKVGAKAAEAVKKTVLELGSNDAYIVLEDADI 246 Query: 250 ELAVKAAVAGRYQNTGQVCAAAKRFIVEEGIAQAFTDRFVAAAAALKMGDPLVEENDLGP 309 + AV+ V GR N G+ C AAKRFIV + I F D +VAA + +GDP+ E+ D+GP Sbjct: 247 DAAVQTCVTGRTYNNGETCIAAKRFIVVDAIYNQFRDAYVAAMKRVTLGDPMGEDADIGP 306 Query: 310 MARFDLRDELHQQVQASVAEGARLLLGGEKIAGEGNYYAATVLADVTPDMTAFRQELFGP 369 MAR DLRD+LHQQV+ S+ GA+LL GGE +G +Y ATVL +V P A+ ELFGP Sbjct: 307 MARKDLRDDLHQQVKDSLEGGAKLLCGGEMPDTDGFFYPATVLENVAPGQPAYDDELFGP 366 Query: 370 VAAITVAKDAAHALALANDSEFGLSATIFTADDTLAAEMAA-RLECGGVFINGYSASDAR 428 VAA+ A+DA A+ +ANDS FGL I T D A +A + G VFING+ + Sbjct: 367 VAALIRAQDADDAMRIANDSRFGLGGGIMTKDTEKALALARDYFDTGMVFINGFGLAIPN 426 Query: 429 VAFGGVKKSGFGRELSHFGLHEFCNVQTV 457 + FGGVK SG+GRE FG+ EF NV++V Sbjct: 427 MPFGGVKDSGYGREHGGFGMKEFVNVKSV 455 Lambda K H 0.319 0.131 0.386 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: 502 Number of extensions: 20 Number of successful extensions: 3 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: 462 Length of database: 459 Length adjustment: 33 Effective length of query: 429 Effective length of database: 426 Effective search space: 182754 Effective search space used: 182754 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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