Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate WP_011383257.1 AMB_RS04160 NAD-dependent succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >NCBI__GCF_000009985.1:WP_011383257.1 Length = 499 Score = 625 bits (1613), Expect = 0.0 Identities = 306/480 (63%), Positives = 375/480 (78%), Gaps = 1/480 (0%) Query: 5 DAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAW 64 D L + AYVDG WV AD+G+ V +PATG +I SVP +GA ETRRAI+AA+ A W Sbjct: 19 DPSLIKSHAYVDGVWVGADDGRRFDVLDPATGGLIASVPDLGATETRRAIDAAEAAWNPW 78 Query: 65 RALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAK 124 R TAK+RA + W DL++ +QD LARL++ EQGKPLAEA GEI+Y ASF+ WF EE K Sbjct: 79 RQRTAKDRAAVMMAWHDLIMAHQDALARLLSAEQGKPLAEAMGEISYGASFISWFAEEGK 138 Query: 125 RIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQ 184 R YGD IP D+R++V+KQPIGV AA+TPWNFP AMITRK PALAAGC +V+KPA Sbjct: 139 RAYGDLIPTTASDRRLLVMKQPIGVVAAVTPWNFPMAMITRKCAPALAAGCPVVVKPAED 198 Query: 185 TPYSALALAELAERAGIPKGVFSVVTG-SAGEVGGELTSNPIVRKLTFTGSTEIGRQLMA 243 TP SALALAELA RAG+PKG+F++VT VGGE+T N VRKL+FTGST +G+ LMA Sbjct: 199 TPLSALALAELAHRAGLPKGLFNIVTTRQPAAVGGEMTGNAKVRKLSFTGSTRVGKLLMA 258 Query: 244 ECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYD 303 +CA+ +KKVSLELGGNAPFIVFDD DLDAAV GAL SKYRN+GQTC+C NR VQ G+Y+ Sbjct: 259 QCAETVKKVSLELGGNAPFIVFDDCDLDAAVAGALASKYRNSGQTCICTNRFLVQAGIYE 318 Query: 304 AFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHAL 363 F KL A + +G+ L V GPLI+A AVAKV H+ADAVSKGA+V++GG+PHAL Sbjct: 319 DFAVKLAEKAAAMAVGHALSGVVQQGPLINAAAVAKVAAHVADAVSKGARVLTGGRPHAL 378 Query: 364 GGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDL 423 GG F++PT+L DV L ++ETFGP+AP+ RF+ EAE IA++N +EFGLA YFY+RD+ Sbjct: 379 GGGFWQPTVLADVTPAMLCFREETFGPVAPLLRFETEAEAIALANASEFGLAGYFYSRDV 438 Query: 424 ARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGGI 483 ARVFRVAE LE GMVG+N LISNEVAPFGGIK SGLGREGSKYG++D++E KY+C+GG+ Sbjct: 439 ARVFRVAEALECGMVGVNESLISNEVAPFGGIKESGLGREGSKYGLDDFMETKYVCIGGL 498 Lambda K H 0.317 0.135 0.391 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: 700 Number of extensions: 12 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: 483 Length of database: 499 Length adjustment: 34 Effective length of query: 449 Effective length of database: 465 Effective search space: 208785 Effective search space used: 208785 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