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 BPHYT_RS22430 BPHYT_RS22430 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__BFirm:BPHYT_RS22430 Length = 486 Score = 369 bits (948), Expect = e-106 Identities = 206/483 (42%), Positives = 276/483 (57%), Gaps = 5/483 (1%) Query: 1 MANVTYTDTQLL-----IDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAA 55 M ++ D LL I GEW A G T +V NPATG+ I V G A+ RA+ A Sbjct: 1 MTTLSLKDPSLLKSHAYIAGEWQGADDGTTFEVKNPATGETIATVPRMGTAETRRAIDTA 60 Query: 56 QSGFEAWRKVPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIE 115 + + AWR A +RA +RK L+ E AD +A+++T EQGKPL EA+ E+ AA +E Sbjct: 61 NAAWPAWRATTAKQRAVILRKWHDLMMENADDLAKILTTEQGKPLAEAKGEIQYAASFLE 120 Query: 116 WFADEGRRVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSF 175 WFA+EG+RV G +P + V KEP+G AA TPWNFP + RK+ ALA GC Sbjct: 121 WFAEEGKRVNGDTIPTPASDKRIVVTKEPIGVCAAITPWNFPAAMITRKVGPALAAGCPI 180 Query: 176 LVKAPEETPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPV 235 +VK E TP S AL AGVP GV +V G+P I + + +P++RK++FTGSTPV Sbjct: 181 IVKPAEATPLSALALAVLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPV 240 Query: 236 GKQLASLAGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLV 295 G+ L + +K+ ++ELGG+AP IV +DAD+ AV A +K+RN+GQ C+ RF V Sbjct: 241 GRLLMAQCAPTVKKVSLELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYV 300 Query: 296 HNSIRDEFTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETG 355 H+ + D F L E LKVG G E+G T G L N + + S I++A GA I TG Sbjct: 301 HDKVYDAFAEKLRVAVEQLKVGRGTEDGVTQGPLINDAAVLKVESHIEDALAKGARIVTG 360 Query: 356 GERIGSEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGY 415 G+R FF PTV+A+V V +E FGP+A + F EE I AN FGLA Y Sbjct: 361 GKRHALGHGFFEPTVLADVTPAMKVARDETFGPLAPLFRFSSDEEVIRLANDTEFGLASY 420 Query: 416 AFTRSFANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKS 475 ++R V + + LE GM+ IN PFGGVK SG G EG ++ Y+V K Sbjct: 421 FYSRDIGRVWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYVVIKY 480 Query: 476 VTV 478 + V Sbjct: 481 LCV 483 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: 633 Number of extensions: 26 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: 486 Length adjustment: 34 Effective length of query: 447 Effective length of database: 452 Effective search space: 202044 Effective search space used: 202044 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