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 YP_004142598.1 Mesci_3425 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000185905.1:YP_004142598.1 Length = 485 Score = 385 bits (990), Expect = e-111 Identities = 207/467 (44%), Positives = 281/467 (60%) Query: 12 LIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERA 71 LI+GEWV A SG+T+DV NPATG IG V +G A+ RA+ AA F+ WRK A ER+ Sbjct: 14 LINGEWVQADSGQTVDVNNPATGLKIGTVPKSGKAETRRAIEAAAEAFKTWRKTTALERS 73 Query: 72 ATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPP 131 +RK + + D +A+L+T EQGK L E++ E+ SAA I WFA+EGRR YG +VP Sbjct: 74 KLLRKLHDAMMDNQDVLAELLTIEQGKSLFESKGEIGSAASYILWFAEEGRRTYGDVVPS 133 Query: 132 RNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALL 191 + V KEPVG +AA TPWNFP + + RKL ALA GC+ +VK +TP S A Sbjct: 134 PWADRRILVTKEPVGVIAAITPWNFPSSMLARKLGPALAAGCTAVVKPASQTPYSGLAWG 193 Query: 192 RAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRAT 251 + G P GV+ ++ G +EI + +P++ K+TFTGST VGK L + + +K+ + Sbjct: 194 ALAEEVGFPKGVVNILTGSASEIGDEICANPLVSKITFTGSTEVGKLLIQKSSVTVKKVS 253 Query: 252 MELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHA 311 MELGG+AP IV +DAD+ AV A AK+RN+GQ C+ RFLV + D+F L + Sbjct: 254 MELGGNAPFIVFDDADLERAVAGAITAKYRNSGQTCVCTNRFLVQAGVYDKFVEKLAAAS 313 Query: 312 EGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVI 371 LKVG+GLE+G G L + + + + +I +A G I GG+R G+FF PTVI Sbjct: 314 NALKVGSGLEDGVQQGPLIDEKAVEKVEELIADATSKGGKIVAGGKRHALGGSFFQPTVI 373 Query: 372 ANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRL 431 AN E FGPVA + F+ EEA+A AN FGLA Y +T + + L Sbjct: 374 ANATPKMRFMKEEIFGPVAPVFKFETEEEAVALANDTEFGLACYFYTGDLGRAFRVMEGL 433 Query: 432 EVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 + GM+ +N+ PE PFGGVK+SG G EGG + +E YL TK V + Sbjct: 434 KYGMVGVNEGLITTPEAPFGGVKESGLGKEGGHQGIEDYLDTKYVCI 480 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: 661 Number of extensions: 24 Number of successful extensions: 1 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 24 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