Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate GFF2064 HP15_2020 succinate-semialdehyde dehydrogenase I
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Marino:GFF2064 Length = 489 Score = 653 bits (1684), Expect = 0.0 Identities = 311/486 (63%), Positives = 392/486 (80%), Gaps = 3/486 (0%) Query: 1 MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60 ++LK+ +L R+QAY++G W+ A +G+T VN+PA GE + +VP M + R AIEAA A Sbjct: 3 LELKNRELLREQAYINGQWITAKSGKTFAVNDPANGEQLATVPDMDDTDARAAIEAASAA 62 Query: 61 LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120 PAWR+ AKERAN LR+WF+L++ NQ+DLARLMT EQGKPLAE++GE+ Y ASF+EWF Sbjct: 63 WPAWRSTPAKERANILRKWFNLLMANQEDLARLMTAEQGKPLAESRGEVGYGASFIEWFA 122 Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 EEAKR YGD IPGH DKRI+VIKQP+GV AAITPWNFP AMITRK PALAAGC +V+K Sbjct: 123 EEAKRAYGDVIPGHGKDKRIVVIKQPVGVVAAITPWNFPIAMITRKVAPALAAGCPVVVK 182 Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGS---AGEVGGELTSNPIVRKLTFTGSTEI 237 PA TP SALA+ LAE AG+P G+ +++T S A VG ELT NPIVRK++FTGST + Sbjct: 183 PAEDTPLSALAITALAEEAGVPAGLINIITCSKPNAVSVGSELTGNPIVRKVSFTGSTPV 242 Query: 238 GRQLMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYV 297 G+ LM + + +KKVSLELGGNAPFIVFDDADLDAAV G + SKYRN GQTCVCANR+YV Sbjct: 243 GKLLMRQASDTVKKVSLELGGNAPFIVFDDADLDAAVAGLMASKYRNTGQTCVCANRVYV 302 Query: 298 QDGVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSG 357 Q GVYDAF +KLKAAV+K+ +G GLE GPLI+ A+AKV+ HI DA SKGAKV G Sbjct: 303 QAGVYDAFAEKLKAAVSKMVVGPGLEGETQQGPLINDAALAKVKRHIEDATSKGAKVALG 362 Query: 358 GKPHALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASY 417 G+ H+LGGTFFEPTIL + L++++ETFGP+AP+F+F+ + E IAM+ND+EFGL++Y Sbjct: 363 GRAHSLGGTFFEPTILTHATQEMLIAREETFGPVAPLFKFETDDEAIAMANDSEFGLSAY 422 Query: 418 FYARDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY 477 FY+R++ RV+RVAE+LE GM+G+N G+IS EVAPFGG+K SGLGREGS YG+++Y+E+KY Sbjct: 423 FYSRNIHRVWRVAEELESGMIGVNEGIISTEVAPFGGVKESGLGREGSHYGLDEYMELKY 482 Query: 478 LCLGGI 483 LCLGG+ Sbjct: 483 LCLGGM 488 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: 727 Number of extensions: 10 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: 489 Length adjustment: 34 Effective length of query: 449 Effective length of database: 455 Effective search space: 204295 Effective search space used: 204295 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