Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_076476004.1 BW971_RS02050 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q8GAI8 (450 letters) >NCBI__GCF_900156495.1:WP_076476004.1 Length = 500 Score = 496 bits (1276), Expect = e-145 Identities = 256/448 (57%), Positives = 324/448 (72%), Gaps = 5/448 (1%) Query: 2 LATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLEM 61 L +A A +DA+ AL+ + AA WA T+PR R+ ILR AFDL+T R+ D ALLMTLEM Sbjct: 51 LTQVADAGPDDAMLALKQSVAAADDWAATSPRERSVILRAAFDLITERAADLALLMTLEM 110 Query: 62 GKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWNF 121 GK L +++ E+AYGAEFLRWFSEE VR GRY +P G +ILV H+PVGPCL ITPWNF Sbjct: 111 GKALPDSKSEIAYGAEFLRWFSEEAVRINGRYTQSPGGTGRILVTHQPVGPCLAITPWNF 170 Query: 122 PLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGIS 181 PLAM TRK+ PA+AAG T+++KPA TPLT A+ EAGLP GVL V+ +S AS + Sbjct: 171 PLAMGTRKIGPALAAGNTIIVKPAAETPLTMLALAKIFAEAGLPPGVLAVLPTSDASAVC 230 Query: 182 GPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEGA 241 PL++D+R+RK++FTGST VG+ L+ A+ +V RTSMELGGNAPF+VF+DADLD A++GA Sbjct: 231 TPLIEDTRIRKITFTGSTGVGRILLGQAAANVQRTSMELGGNAPFIVFDDADLDAALDGA 290 Query: 242 MAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGAR 301 AAKMRN GEACTAANRFLV +SVA+EFT A M AL+ G G + +GPLI+ R Sbjct: 291 FAAKMRNGGEACTAANRFLVHDSVAEEFTDGLIARMQALTVGPGYADGTTLGPLISEKQR 350 Query: 302 DDIHALVTAAVDAGAVAVTGGAPV-----DGPGYFYQPTVLADVPNNAAILGQEIFGPVA 356 + + VT AV GA GG G G+FY PTVL +VP A I EIFGPVA Sbjct: 351 NSVAQKVTDAVADGARVRLGGEQARAEQHGGDGWFYPPTVLDEVPVGAEITRGEIFGPVA 410 Query: 357 PVTTFTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPF 416 ++TF T +AI AN +EYGLAAY+Y+RD +R L V+++++ G+VG N G+IS+ AAPF Sbjct: 411 VISTFGTVDEAIAAANDTEYGLAAYIYTRDLDRALSVSDRLQTGLVGVNRGVISDVAAPF 470 Query: 417 GGVKQSGLGREGGSEGIAEYTTTQYIGI 444 GG KQSGLGREGG EGI E+ TT+Y+ + Sbjct: 471 GGEKQSGLGREGGLEGIGEFLTTKYVAL 498 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: 565 Number of extensions: 19 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: 450 Length of database: 500 Length adjustment: 33 Effective length of query: 417 Effective length of database: 467 Effective search space: 194739 Effective search space used: 194739 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