Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_073950325.1 RH94_RS25575 gamma-aminobutyraldehyde dehydrogenase
Query= SwissProt::Q8GAI8 (450 letters) >NCBI__GCF_001906585.1:WP_073950325.1 Length = 511 Score = 290 bits (742), Expect = 7e-83 Identities = 181/443 (40%), Positives = 249/443 (56%), Gaps = 6/443 (1%) Query: 4 TLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLEMGK 63 T A +D AA+ AA A WA P R++ L R +++ R+EDFA +L+ GK Sbjct: 51 TYELAGPDDVDAAVAAAREAFPGWAGATPGDRSDALHRFAEVLADRAEDFARAESLQCGK 110 Query: 64 PLAEARG-EVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWNFP 122 PL R +V + +F+ G+ G + V+ +P+G I PWN+P Sbjct: 111 PLKLTREFDVPGTIDNAAFFAGAARHLQGQSAGEYSGDHTSYVRREPIGVVGSIAPWNYP 170 Query: 123 LAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGISG 182 L MA KV PA+AAG T+VLKPA+LTPLTS LFAQ EAG+P GV+N+V+ + Sbjct: 171 LQMAAWKVLPAIAAGNTIVLKPAELTPLTSLLFAQAATEAGIPDGVINIVTGTGKEA-GE 229 Query: 183 PLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEGAM 242 L+ + VSFTGST VGKR+ A+ V R +ELGG APFVVF+DADL+ AV GA+ Sbjct: 230 HLVGHPDVAMVSFTGSTAVGKRVAEIATASVKRLHLELGGKAPFVVFDDADLEAAVNGAV 289 Query: 243 AAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGARD 302 A + N G+ CTAA R VQ + +EF + AA M + G P + +GPLI++ RD Sbjct: 290 AGALINTGQDCTAATRAYVQRPLYEEFVARTAALMETVRLGDPFAPGTDLGPLISHVHRD 349 Query: 303 DIHALVTAAVDAGAVAVTGGAPVDGP---GYFYQPTVLADVPNNAAILGQEIFGPVAPVT 359 + V A A A VTGG G G +Y+PT++A ++ I+ EIFGPV V Sbjct: 350 RVAGFVDRA-RAYARVVTGGEAPQGELKNGAYYRPTLIAGAAQDSEIVQSEIFGPVLVVL 408 Query: 360 TFTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGV 419 F ++ + I+LAN + YGLAA +SRD R R +I+ G V N I + P GG Sbjct: 409 PFDSDDEGIRLANDTAYGLAASAWSRDVYRANRATREIKAGCVWVNDHIPIISEMPHGGS 468 Query: 420 KQSGLGREGGSEGIAEYTTTQYI 442 KQSG G++ S EYT +++ Sbjct: 469 KQSGFGKDMSSYSFEEYTQIKHV 491 Lambda K H 0.317 0.131 0.376 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: 472 Number of extensions: 23 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: 450 Length of database: 511 Length adjustment: 34 Effective length of query: 416 Effective length of database: 477 Effective search space: 198432 Effective search space used: 198432 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