Align Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= SwissProt::Q9SAK4 (528 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 349 bits (896), Expect = e-100 Identities = 194/483 (40%), Positives = 291/483 (60%), Gaps = 18/483 (3%) Query: 56 LIGGKWLDSYDNKTIKVNNPATGEIIADVACMGTKETNDAIASSYEAFTSWSRLTAGERS 115 LI G+ ++S TI NPA E+I +A G E A+A++ EAF W+ L A +R+ Sbjct: 5 LINGRQVESAS--TIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQRA 62 Query: 116 KVLRRWYDLLIAHKEELGQLITLEQGKPL---KEAIGEVAYGASFIEYYAEEAKRVYGDI 172 K+LR+ DL+ H +E+ +L +L+ G+ K+ + V A ++A+ V G+ Sbjct: 63 KLLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKML--VPRAADNFYFFADTCCHVDGET 120 Query: 173 IPPNLSDRRLLVLKQPVGVVGAITPWNFPLAMITRKVGPALASGCTVVVKPSELTPLTAL 232 P N D L QPVGVVG I+PWN P T K P LA G T V+K SEL+PL+A Sbjct: 121 YPTN--DHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSAD 178 Query: 233 AAAELALQAGVPPGALNVVMGNAPEIGDALLTSPQVRKITFTGSTAVGKKLMAAAAPTVK 292 +L L+AG+P G N+V G +G+AL+ P VR ++FTGSTA G +++ + +K Sbjct: 179 RLGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSGG--LK 236 Query: 293 KVSLELGGNAPSIVFDDADLDVAVKGTLAAKFRNSGQTCVCANRVLVQDGIYDKFAEAFS 352 K S+ELGG +P+I+FDD D + AV + A + N+G++C R+LVQDG+YD+F A + Sbjct: 237 KYSMELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALA 296 Query: 353 EAVQKLEVGDGFRDGTTQGPLINDAAVQKVETFVQDAVSKGAKIIIGGKRHSLGMT---- 408 E +K+ VGD + T GP+I +KV ++++ +S+GA+++ GG G+ Sbjct: 297 ERTRKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHLK 356 Query: 409 ---FYEPTVIRDVSDNMIMSKEEIFGPVAPLIRFKTEEDAIRIANDTIAGLAAYIFTNSV 465 F PTV+ DV ++ +++EEIFGPVA +IRFK E +A++IAN T GLA+Y++T + Sbjct: 357 NGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENG 416 Query: 466 QRSWRVFEALEYGLVGVNEGLISTEVAPFGGVKQSGLGREGSKYGMDEYLEIKYVCLGDM 525 R+ R+ E +E GLV VN + PFGG+K SG GREG Y + +LE+K VC+ Sbjct: 417 ARAIRMAEGIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNVCVSKG 476 Query: 526 NRH 528 + H Sbjct: 477 SHH 479 Lambda K H 0.317 0.134 0.383 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: 618 Number of extensions: 31 Number of successful extensions: 4 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: 528 Length of database: 485 Length adjustment: 34 Effective length of query: 494 Effective length of database: 451 Effective search space: 222794 Effective search space used: 222794 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