Align Succinate-semialdehyde dehydrogenase; SsaDH; EC 1.2.1.16 (characterized)
to candidate WP_110208547.1 DNK54_RS18780 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q8GAI8 (450 letters) >NCBI__GCF_003194585.1:WP_110208547.1 Length = 490 Score = 456 bits (1173), Expect = e-133 Identities = 238/436 (54%), Positives = 306/436 (70%), Gaps = 2/436 (0%) Query: 12 DAVAALEAACAAQTSWARTAPRVRAEILRRAFDLVTARSEDFALLMTLEMGKPLAEARGE 71 DAV A++AA AA WA TAPR R E LRRAFDL+ A+ E+ A LM E GK LA+AR E Sbjct: 56 DAVRAVDAAEAAAAGWAATAPRERGETLRRAFDLMHAQGEELAGLMAWENGKSLADARAE 115 Query: 72 VAYGAEFLRWFSEETVRDYGRYLTTPEGKNKILVQHKPVGPCLLITPWNFPLAMATRKVA 131 V Y AEF RWF+EE VR G Y ++P G + +V +PVG ++TPWNFP AMATRK+ Sbjct: 116 VTYAAEFFRWFAEEAVRPDGGYGSSPAGGTRTIVTQRPVGIAAMVTPWNFPAAMATRKIG 175 Query: 132 PAVAAGCTMVLKPAKLTPLTSQLFAQTMMEAGLPAGVLNVVSSSSASGISGPLLKDSRLR 191 PA+AAGCT+VLKPA TPLT+ A+ + EAG+P GV+NVV ++ A + L DSR+R Sbjct: 176 PALAAGCTVVLKPAAETPLTALAVARILGEAGVPDGVVNVVPTTRAGDVVSAWLDDSRVR 235 Query: 192 KVSFTGSTPVGKRLMSDASRHVLRTSMELGGNAPFVVFEDADLDKAVEGAMAAKMRNMGE 251 K+SFTGST VG+RL++ A+ V+ TSMELGGNAPFVV DAD++ AV GAM AK RN G+ Sbjct: 236 KISFTGSTGVGRRLLAQAAERVVNTSMELGGNAPFVVGPDADVEAAVTGAMLAKFRNGGQ 295 Query: 252 ACTAANRFLVQESVAQEFTRKFAAAMGALSTGRGTDPASQVGPLINNGARDDIHALVTAA 311 ACTAANRF V E+VA +F +F A + L+ G D SQ+GPLI A+ + ALV+ A Sbjct: 296 ACTAANRFYVHEAVAADFIARFGAEIERLTVGPAFDD-SQIGPLITAQAQQKVTALVSEA 354 Query: 312 VDAGAVAVTGGAPVDGPGYFYQPTVLADVPNNAAILGQEIFGPVAPVTTFTTEQDAIKLA 371 AGA G+ DG G+FY PT++ADVP ++ +L +EIFGPVAPV T+ + + + L Sbjct: 355 TAAGARIAHQGSCPDGAGHFYPPTLVADVPADSPLLSEEIFGPVAPVVTWHDDAEVLALV 414 Query: 372 NASEYGLAAYLYSRDFNRLLRVAEQIEFGMVGFNAGIISNAAAPFGGVKQSGLGREGGSE 431 N +E+GL+AY+Y + L AE++E GMVG N G++S+ AAPFGGVKQSG+GREG E Sbjct: 415 NGTEFGLSAYVYG-ELGWALPFAERVEAGMVGINRGLVSDPAAPFGGVKQSGIGREGAHE 473 Query: 432 GIAEYTTTQYIGIADP 447 GI EY TQY +A P Sbjct: 474 GIREYLETQYFSVAWP 489 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: 559 Number of extensions: 26 Number of successful extensions: 3 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: 490 Length adjustment: 33 Effective length of query: 417 Effective length of database: 457 Effective search space: 190569 Effective search space used: 190569 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