Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_110207112.1 DNK54_RS11350 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q8GAI8 (450 letters) >NCBI__GCF_003194585.1:WP_110207112.1 Length = 461 Score = 449 bits (1156), Expect = e-131 Identities = 239/444 (53%), Positives = 298/444 (67%), Gaps = 3/444 (0%) Query: 2 LATLASATSEDAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLEM 61 + T+ + DAVAA++AA AA +WA T R R E LRR FDL+ +E L+ E Sbjct: 17 IETVPDSNVLDAVAAVDAAAAAFPAWAATPARTRGETLRRCFDLMLRDAELLVGLIAGEN 76 Query: 62 GKPLAEARGEVAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWNF 121 GK LA+AR EV Y AEF RWFSEE VR G Y P GK K LV PVG L+TPWNF Sbjct: 77 GKSLADARAEVNYAAEFFRWFSEEAVRSEGTYGDAPAGKAKTLVTRAPVGVAALVTPWNF 136 Query: 122 PLAMATRKVAPAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGIS 181 P AMATRK+APA+AAGCT+VLKPA TPLT+ A+ M EAG+P GV+NVV ++ A+ + Sbjct: 137 PAAMATRKIAPALAAGCTVVLKPAAETPLTALALAEIMREAGVPDGVVNVVPTTDAAAVV 196 Query: 182 GPLLKDSRLRKVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEGA 241 L+D R+RK+SFTGST VG+ L+ A+ VL SMELGGNAPFV+ DAD+D AV GA Sbjct: 197 TAWLEDPRIRKISFTGSTGVGRALLRQAADRVLNASMELGGNAPFVITADADVDAAVAGA 256 Query: 242 MAAKMRNMGEACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGAR 301 M AK R G+ACTAANRF V +A EF KF A+ AL G D +QVGP+I+ A Sbjct: 257 MIAKFRGGGQACTAANRFYVHRDIAAEFVEKFGDAVAALRVGPAADETNQVGPVISEKAL 316 Query: 302 DDIHALVTAAVDAGA-VAVTGGAPVDGPGYFYQPTVLADVPNNAAILGQEIFGPVAPVTT 360 + LV AAV GA +AV G P G+F+ PT+L DVP A IL +EIFGPVAP+ T Sbjct: 317 GTLTTLVDAAVADGARIAVQGTVP--EKGWFFPPTILVDVPVGAPILSEEIFGPVAPIVT 374 Query: 361 FTTEQDAIKLANASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGVK 420 +T E + ++ N +E+GLAAY+Y+ LR+ EQI+ GMVG N GI+S+ AAPFGGVK Sbjct: 375 WTDEAEMLESVNDTEFGLAAYVYAGRLQDALRLGEQIDAGMVGINRGIVSDPAAPFGGVK 434 Query: 421 QSGLGREGGSEGIAEYTTTQYIGI 444 QSG+GREG EG+ EY T+Y + Sbjct: 435 QSGIGREGAHEGMREYQETRYYSV 458 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: 544 Number of extensions: 23 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: 461 Length adjustment: 33 Effective length of query: 417 Effective length of database: 428 Effective search space: 178476 Effective search space used: 178476 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