Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate GFF3462 HP15_3404 succinic semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Marino:GFF3462 Length = 483 Score = 404 bits (1038), Expect = e-117 Identities = 210/463 (45%), Positives = 289/463 (62%), Gaps = 2/463 (0%) Query: 14 YVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRALTAKERA 73 Y+ G W D ++G T V NPATG++I V M E A+ + AL + + R Sbjct: 13 YIGGRWTDNEHGNTFDVYNPATGKVIAQVASMSEDEVNAAVASGKSALRLTSPYSIETRR 72 Query: 74 NKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRIYGDTIPG 133 L D + N++++ R++ +E GKPL EA+GE+ YAA F ++ + + + TIP Sbjct: 73 KWLEDIRDALKANKEEVGRILCMEHGKPLQEAQGEVDYAAGFFDYCSKHIQALDAHTIPE 132 Query: 134 HQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTPYSALALA 193 D V +PIGVT ITPWNFP MI +K ALAAGC V+KPAS+TP + +AL Sbjct: 133 KPKDCTWTVHYRPIGVTGLITPWNFPIGMIAKKLSAALAAGCPSVIKPASETPLTMIALF 192 Query: 194 ELAER-AGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAECAQDIKKV 252 L ++ IP G+ ++V G A +G L +P V L+FTGSTE+GR+L+ + A +KK+ Sbjct: 193 SLMDKHTDIPDGMVNLVMGKASVIGKVLCESPDVPMLSFTGSTEVGRKLIVDTADQVKKL 252 Query: 253 SLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAFVDKLKAA 312 +LELGGNAPFIVFDDADLDAA + + +K+R GQTCVCANR++V + V DAF +KL Sbjct: 253 ALELGGNAPFIVFDDADLDAAADNLIANKFRGGGQTCVCANRIFVHEKVADAFGEKLAER 312 Query: 313 VAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALGG-TFFEPT 371 V K+ +G+G+ V GPLI+ KV+ H+ DA+ KGA +V+G KP LG FF PT Sbjct: 313 VNKMTVGDGINGDVDLGPLINQAGYDKVKRHVQDALEKGATLVAGKKPEDLGNDLFFPPT 372 Query: 372 ILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDLARVFRVAE 431 ++ V ++ ++ETFGPL P+ F+ E EVI NDTEFGLASY + D R RVA Sbjct: 373 VVHGVNRDMCCYQEETFGPLVPMALFRTEEEVIEAGNDTEFGLASYVFTNDAERAQRVAA 432 Query: 432 QLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLE 474 L +G G NTG APFGG+KASG+GREG G+ +++E Sbjct: 433 GLRFGHCGWNTGTGPTPEAPFGGMKASGIGREGGLEGLFEFVE 475 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: 642 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: 483 Length of database: 483 Length adjustment: 34 Effective length of query: 449 Effective length of database: 449 Effective search space: 201601 Effective search space used: 201601 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