Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate RR42_RS24555 RR42_RS24555 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__Cup4G11:RR42_RS24555 Length = 494 Score = 628 bits (1619), Expect = 0.0 Identities = 305/478 (63%), Positives = 375/478 (78%) Query: 2 QLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKAL 61 +L+D L +A++ W +A G++ V NPATGEI+ V + AE AI A+ +A Sbjct: 14 RLRDPSLLETRAWLASGWQEASGGRSFAVTNPATGEILARVASLSGAEVESAITASAQAQ 73 Query: 62 PAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGE 121 W+ ++ ERA LR WFDLMI N DDLA +MT EQGKPLAEA+GEI YAASF+EWF E Sbjct: 74 AVWQRRSSHERAKLLRAWFDLMIANADDLALIMTSEQGKPLAEARGEILYAASFVEWFAE 133 Query: 122 EAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKP 181 EAKRIYGD P Q DKRI+VI+QP+GV AAITPWNFP+AMITRK PALAAGC+++++P Sbjct: 134 EAKRIYGDVAPHPQTDKRILVIRQPVGVCAAITPWNFPAAMITRKVAPALAAGCSIIVRP 193 Query: 182 ASQTPYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQL 241 A TP +ALALA LAERAGIP GV +V G + E+G LT++P+VRKL+FTGSTE+GR L Sbjct: 194 ADLTPLTALALAVLAERAGIPAGVLQMVCGPSREIGAVLTASPVVRKLSFTGSTEVGRVL 253 Query: 242 MAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGV 301 M++ + IK++SLELGGNAPFIVFDDADLDAA+EGA+ SKYRN+GQTCVCANR VQDG+ Sbjct: 254 MSQSSPTIKRLSLELGGNAPFIVFDDADLDAAIEGAMASKYRNSGQTCVCANRFLVQDGI 313 Query: 302 YDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPH 361 YD FV+ L VA+L +GNG+E GV GPLI A ++ I DAV KGAKVV GGK H Sbjct: 314 YDRFVEALVRRVAELKVGNGVEPGVQQGPLIQKSACEHLQAMIDDAVGKGAKVVVGGKGH 373 Query: 362 ALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYAR 421 ALGGTFFEPT++ + V+++E FGP+APVFRF+DEAE IA++NDTE+GLA+Y Y R Sbjct: 374 ALGGTFFEPTVIAGATPDMRVAREELFGPVAPVFRFRDEAEAIALANDTEYGLAAYLYTR 433 Query: 422 DLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLC 479 D AR++RV E LEYGMVG+NTGLISNEVAPFGG+K SGLGREGS+YGI++YLEIKYLC Sbjct: 434 DNARIWRVGEALEYGMVGLNTGLISNEVAPFGGVKQSGLGREGSRYGIDEYLEIKYLC 491 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: 687 Number of extensions: 14 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: 494 Length adjustment: 34 Effective length of query: 449 Effective length of database: 460 Effective search space: 206540 Effective search space used: 206540 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