Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__PV4:5210745 Length = 485 Score = 340 bits (872), Expect = 6e-98 Identities = 189/473 (39%), Positives = 265/473 (56%), Gaps = 8/473 (1%) Query: 8 DTQLL-----IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAW 62 DTQL+ IDG W + DVVNPA+ + I +V A + D A+ AA+ W Sbjct: 6 DTQLIKLSSYIDGRWT--VGEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEW 63 Query: 63 RKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGR 122 K A+ERAA MRK L+ E + + +L+T EQGKPL EA+ E+ A I+WFA+EG+ Sbjct: 64 SKRSANERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGK 123 Query: 123 RVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEE 182 RVYG +P + V+K+PVG VA+ TPWNFP + RK +AALA GC+F+ + Sbjct: 124 RVYGDTIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPL 183 Query: 183 TPASPAALLRAFVDAGVPAGVIGLVYGDPAE-ISSYLIPHPVIRKVTFTGSTPVGKQLAS 241 TP S A+ AG+PAGV +V G+ A + L HP + K TFTGST VGK L + Sbjct: 184 TPLSALAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLA 243 Query: 242 LAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRD 301 +K+ +MELGG+AP IV +DAD+ AV+ A +K+RNAGQ C+ R V + Sbjct: 244 QCATSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAA 303 Query: 302 EFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGS 361 FT LK+G+GL +G T+G + + + + ++D+ GA + TGG+ Sbjct: 304 AFTEKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSEL 363 Query: 362 EGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSF 421 +F AP ++ +V + + NE FGPV I FD EA+A AN +GLA Y + R Sbjct: 364 GESFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDI 423 Query: 422 ANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTK 474 + + + LE GM+ +N+ PFGGVK SG G EG L+ YL K Sbjct: 424 GRIFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIK 476 Lambda K H 0.318 0.134 0.393 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: 627 Number of extensions: 29 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: 481 Length of database: 485 Length adjustment: 34 Effective length of query: 447 Effective length of database: 451 Effective search space: 201597 Effective search space used: 201597 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