Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate BPHYT_RS30285 BPHYT_RS30285 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__BFirm:BPHYT_RS30285 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:
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