Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate BPHYT_RS30285 BPHYT_RS30285 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >lcl|FitnessBrowser__BFirm:BPHYT_RS30285 BPHYT_RS30285 succinate-semialdehyde dehydrogenase Length = 490 Score = 542 bits (1397), Expect = e-159 Identities = 268/481 (55%), Positives = 343/481 (71%), Gaps = 4/481 (0%) Query: 7 KLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWRA 66 +L R Q +DGAW A +G V NPATGE I V GAA+ R A +AA +A PAWR Sbjct: 9 ELIRPQNLIDGAWTGAADGARFAVTNPATGETIVEVADSGAADARAATDAAARAFPAWRD 68 Query: 67 LTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKRI 126 +ERA LRRW L++ N DDLA+LM++EQGKPLAEA+GE+AY AS++ WF +EA RI Sbjct: 69 TLPRERAEILRRWHALIVANTDDLAKLMSMEQGKPLAEARGEVAYGASYVAWFADEATRI 128 Query: 127 YGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQTP 186 YGD IP Q KR+ +K+P+GV AAITPWNFP AMI RK PALAAGCT+V KPA TP Sbjct: 129 YGDLIPQQQRGKRMSAVKEPVGVIAAITPWNFPLAMIARKIAPALAAGCTVVAKPAEDTP 188 Query: 187 YSALALAELAERAGIPKGVFSVVTGSAGE---VGGELTSNPIVRKLTFTGSTEIGRQLMA 243 +ALALA LA+ AG+P GV ++++ S + + ++ VRK+TFTGST +G+ L Sbjct: 189 LTALALAVLAQEAGLPDGVLNMLSASREQGIAAVADWLADSRVRKITFTGSTPVGKHLAR 248 Query: 244 ECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYD 303 E A +KK+SLELGGNAPFIVFDDADLDAAV G + +K+RN GQTCVC NR+YVQ GVY+ Sbjct: 249 ESAGTLKKLSLELGGNAPFIVFDDADLDAAVTGLMAAKFRNGGQTCVCPNRVYVQAGVYE 308 Query: 304 AFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKP-HA 362 F D L V L + + GP+I+ +A+ K+ H+ DAV GAKV+ GGK Sbjct: 309 RFADLLAKRVGALKVAPATDPQAQIGPMINERAIQKIARHVEDAVKHGAKVLVGGKRLTE 368 Query: 363 LGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARD 422 LG ++ PT+L D + LVS +ETFGP+AP+FRF +EAE I +SNDT FGLA+YFY +D Sbjct: 369 LGPNYYAPTVLTDARDDMLVSCEETFGPVAPLFRFNEEAEAIRLSNDTPFGLAAYFYTQD 428 Query: 423 LARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLGG 482 + R+ RVA QLE G++GIN G +S+E APFGG+K SG GREGSKYG++DY+ IKY+C GG Sbjct: 429 VRRINRVAAQLEAGVIGINEGAVSSEAAPFGGVKESGYGREGSKYGLDDYMSIKYMCQGG 488 Query: 483 I 483 + Sbjct: 489 L 489 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: 665 Number of extensions: 13 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: 490 Length adjustment: 34 Effective length of query: 449 Effective length of database: 456 Effective search space: 204744 Effective search space used: 204744 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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