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_043879642.1 AZC_RS20260 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000010525.1:WP_043879642.1 Length = 493 Score = 369 bits (947), Expect = e-106 Identities = 201/472 (42%), Positives = 271/472 (57%) Query: 10 QLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHE 69 Q LI G WVDA SG TI+V NPATG IG + AG A+ RA+ AA F+ WR A E Sbjct: 22 QNLIGGAWVDADSGATIEVNNPATGAIIGTIPQAGRAETRRAIEAAADAFKIWRAKTAAE 81 Query: 70 RAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIV 129 RA+ + K A ++ D +A+L+T EQGKP EA+ EV ++A + WFA+E RR+YG + Sbjct: 82 RASALHKLADIILANQDDLARLLTTEQGKPFAEAKGEVGASAAYVRWFAEEARRLYGDTI 141 Query: 130 PPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAA 189 P G + V KEPVG VAA TPWNFP + + RK+ AALA GC+ + K E TP S A Sbjct: 142 PSPWAGRRIMVTKEPVGVVAAITPWNFPSSMLARKVGAALAAGCTVVAKPAELTPYSGLA 201 Query: 190 LLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKR 249 AG+PAG + +V GD EI + +P+++KVTFTGSTPVGK L + MK+ Sbjct: 202 WGVLAEMAGIPAGCVNIVTGDAKEIGLEMTSNPIVKKVTFTGSTPVGKLLMKQSADTMKK 261 Query: 250 ATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVK 309 +MELGG+AP IV +DAD+ AV+ A +KFRN+GQ C+ R V I D F + Sbjct: 262 ISMELGGNAPFIVFDDADLDAAVEGAIASKFRNSGQTCVCANRIYVQAGIHDAFAEKFAE 321 Query: 310 HAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNFFAPT 369 LK+GNG ++G G L + + + ++ +A G +I TGG+R FF PT Sbjct: 322 AVRKLKIGNGFDDGVVAGPLIEEKAVAKVERLLKDATDKGGTIVTGGKRSPLGLTFFEPT 381 Query: 370 VIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHLLTQ 429 VIAN D E FGP+A + F+ EE + AN +GLA Y FT+ +++ Sbjct: 382 VIANATQDMGFAREEIFGPMAPLFKFETEEEVVRYANSTEYGLACYFFTKDLGRAFRVSE 441 Query: 430 RLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMAV 481 LE G + +N PFGGVK+SG G EG + YL K + + V Sbjct: 442 ALEYGQVGVNAGVITTEVAPFGGVKESGVGREGSKYGCDDYLNIKYICIGGV 493 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: 705 Number of extensions: 35 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: 493 Length adjustment: 34 Effective length of query: 447 Effective length of database: 459 Effective search space: 205173 Effective search space used: 205173 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