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 WP_022949919.1 H035_RS0115725 aldehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000421465.1:WP_022949919.1 Length = 476 Score = 215 bits (548), Expect = 2e-60 Identities = 147/470 (31%), Positives = 226/470 (48%), Gaps = 17/470 (3%) Query: 19 DAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFE---AWRKVPAHERAATMR 75 DA S + V +P +P+G V +++AL + + + W +PA ERAA + Sbjct: 9 DAPSAGNLRVFSPFENRPVGSVETVDAVGVEQALENSTALYRDRTGW--LPAGERAAILE 66 Query: 76 KAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVPPRNLG 135 + AAL+ ERA+ + + E GKP + R E+ A D I + R +G +P + Sbjct: 67 RTAALMTERAEQLIAVAIAEGGKPYQDTRAELRRAIDGIHNCRECIRSGHGSEIPMQIND 126 Query: 136 AQQTVV----KEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAALL 191 A + +EP+GPV A + +N P+N +V ++ A+A GC +VK E+TP S AL+ Sbjct: 127 ASMHRLAFTHREPIGPVVAVSAFNHPLNLIVHQVGPAIAAGCPVIVKPAEKTPLSAFALV 186 Query: 192 RAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRAT 251 +AG+P + + I+ L+ + +F GS+ VG L S R Sbjct: 187 ELLREAGLPEAWCQPLMPEKLSIAEALVTDARVAFFSFIGSSKVGWHLRSKLA-RGTRCA 245 Query: 252 MELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKHA 311 +E GG APV+ AEDAD+ + F +AGQVC+S R H SI E L + A Sbjct: 246 LEHGGAAPVVAAEDADLDAMLPLLTKGGFYHAGQVCVSVQRVYAHRSIARELAEKLARSA 305 Query: 312 EGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPTVI 371 + LKVG+ + T +G L + + ++ A GA + GGER+ + PTV+ Sbjct: 306 DALKVGDPTDLDTEVGPLIRREEVDRVDKWVNEAVTEGAELLAGGERLSEA--CYRPTVL 363 Query: 372 ANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQRL 431 N + V E FGPV + +D+++EAIA AN LP+ T S + L Sbjct: 364 FNPADSSKVSRLEIFGPVVCVYEYDEIDEAIARANALPYAFQAAVMTGSLDTAMHAFKHL 423 Query: 432 EVGMLWINQPA---TPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTV 478 + + IN W MPF G+K+SGYG+ G P + K + Sbjct: 424 QASAVMINDHTAFRVDW--MPFAGLKESGYGTGGIPYTYREMQIEKMAVI 471 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: 606 Number of extensions: 35 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: 481 Length of database: 476 Length adjustment: 34 Effective length of query: 447 Effective length of database: 442 Effective search space: 197574 Effective search space used: 197574 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: 51 (24.3 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