Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate H281DRAFT_02680 H281DRAFT_02680 succinate semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Burk376:H281DRAFT_02680 Length = 492 Score = 669 bits (1726), Expect = 0.0 Identities = 328/482 (68%), Positives = 385/482 (79%) Query: 2 QLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKAL 61 +L D L R AY+DG W AD+ +T V++PATGE I VP M AETRRAIEA + A Sbjct: 11 RLADPSLLRTLAYIDGQWCGADDARTFAVDDPATGEKIADVPLMTGAETRRAIEAGEHAQ 70 Query: 62 PAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGE 121 WR LTA +R+ L+RW LMI N DDLA +M+ EQGKPLAEAKGEI YAASF+EWF E Sbjct: 71 RGWRKLTAAQRSTILKRWHALMIANTDDLAIIMSAEQGKPLAEAKGEIGYAASFIEWFAE 130 Query: 122 EAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKP 181 +AKR+ GD + DKR++V K+PIGV AAITPWNFP+AMITRK PALAAGC M+LKP Sbjct: 131 QAKRVDGDVLASPAADKRMLVTKEPIGVCAAITPWNFPAAMITRKVAPALAAGCAMILKP 190 Query: 182 ASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQL 241 A TP SALALAELA RAG+P GVFSVV G +G E+TSNPIVRKL+FTGST +GR L Sbjct: 191 AEATPLSALALAELAHRAGVPAGVFSVVVGDPRSIGAEMTSNPIVRKLSFTGSTPVGRML 250 Query: 242 MAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGV 301 M++CA +KK+SLELGGNAPFIVFDDADLDAAVEGAL SKYRN GQTCVC NR+YVQDGV Sbjct: 251 MSQCAPTVKKLSLELGGNAPFIVFDDADLDAAVEGALASKYRNAGQTCVCTNRVYVQDGV 310 Query: 302 YDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPH 361 YDAF +K AAV ++ +GNG E+GVT GPLI+ AV KVE HIADAV+ GA+V++GGK H Sbjct: 311 YDAFAEKFAAAVGRIKVGNGFESGVTQGPLINEAAVEKVEAHIADAVAHGARVLTGGKRH 370 Query: 362 ALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYAR 421 A G FFEPT++ DV + +ETFGP+AP+FRF +E E IA +N TEFGLA+YFY+R Sbjct: 371 AAGKLFFEPTVVGDVTARMRFATEETFGPVAPLFRFTNEREAIAAANATEFGLAAYFYSR 430 Query: 422 DLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCLG 481 D+ R++RVAE LEYGMVGINTGLISNEVAPFGG+K SGLGREGSKYGIEDYLEIKYLC+G Sbjct: 431 DIGRIWRVAEALEYGMVGINTGLISNEVAPFGGVKQSGLGREGSKYGIEDYLEIKYLCMG 490 Query: 482 GI 483 G+ Sbjct: 491 GL 492 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: 711 Number of extensions: 13 Number of successful extensions: 1 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: 492 Length adjustment: 34 Effective length of query: 449 Effective length of database: 458 Effective search space: 205642 Effective search space used: 205642 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