Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate RR42_RS21375 RR42_RS21375 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Cup4G11:RR42_RS21375 Length = 488 Score = 686 bits (1770), Expect = 0.0 Identities = 339/486 (69%), Positives = 396/486 (81%), Gaps = 3/486 (0%) Query: 1 MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60 MQLKD L R QA++ G W AD+G T V NPA G +IG+VP MGAAET RAIEAA A Sbjct: 1 MQLKDPTLLRSQAFIGGQWQSADSGATFPVTNPADGSLIGTVPLMGAAETTRAIEAARVA 60 Query: 61 LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120 AWR TA+ERA LR W+DLM+ N DDLA LMT EQGKPLAEA+GE YAASFLEWF Sbjct: 61 QAAWRRKTARERAQVLRAWYDLMLANADDLAVLMTTEQGKPLAEARGEAVYAASFLEWFA 120 Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 E+AKR++GD + DKR++V+K+P+GV AAITPWNFP AMITRKAGPALAAGC MVLK Sbjct: 121 EQAKRVHGDVLATPASDKRLLVVKEPVGVCAAITPWNFPLAMITRKAGPALAAGCAMVLK 180 Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAG---EVGGELTSNPIVRKLTFTGSTEI 237 PA TP SALALA LAERAG+P G+ SVVTG A E+G ELT +P+VRKL+FTGSTE+ Sbjct: 181 PAEDTPLSALALALLAERAGLPAGLLSVVTGDAASSIEIGAELTGSPVVRKLSFTGSTEV 240 Query: 238 GRQLMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYV 297 GR LM + A IKK+SLELGGNAPFIVFDDADLDAAVEGA+ SKYRN GQTCVCANRLYV Sbjct: 241 GRILMRQSAPTIKKLSLELGGNAPFIVFDDADLDAAVEGAMASKYRNAGQTCVCANRLYV 300 Query: 298 QDGVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSG 357 D VYDAF KL AAV L +G+GLE GV GPLI+ AVAKVE+HIADA+ KGA++++G Sbjct: 301 HDKVYDAFAQKLVAAVKTLKVGHGLEPGVQQGPLINEDAVAKVEQHIADALGKGARLLTG 360 Query: 358 GKPHALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASY 417 GK H LGGTFFEPT+L +V + +V+K ETFGPLAP+FRF + EV+ M+NDTEFGLASY Sbjct: 361 GKRHDLGGTFFEPTVLANVTPDMVVAKQETFGPLAPLFRFTSDEEVVNMANDTEFGLASY 420 Query: 418 FYARDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY 477 F++RD+ R++RVAE LEYGMVGINTGLISNEVAPFGG+K SGLGREG+ YGIE+YLE+KY Sbjct: 421 FFSRDIGRIWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGASYGIEEYLEVKY 480 Query: 478 LCLGGI 483 LC+GG+ Sbjct: 481 LCMGGV 486 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: 715 Number of extensions: 14 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: 488 Length adjustment: 34 Effective length of query: 449 Effective length of database: 454 Effective search space: 203846 Effective search space used: 203846 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