Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__azobra:AZOBR_RS22315 Length = 497 Score = 283 bits (724), Expect = 9e-81 Identities = 159/458 (34%), Positives = 255/458 (55%), Gaps = 10/458 (2%) Query: 14 YINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERS 73 + GE+ A +G+ V NPATGE + A+ A+ AA A W +ER Sbjct: 23 FFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAAVAAQKEWAKRPVRERG 82 Query: 74 AKLRRWFELMIENQDDLARLMTTEQGKPL-AEAKGEIAYAASFIEWFAEEAKRIYGDTIP 132 + ++ +++++A+L+ E GK L E++ E + +F A + G+TIP Sbjct: 83 KLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFGGLAPELKGETIP 142 Query: 133 GHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALAL 192 P + +++P+GV AI PWN P ++ K PA+ AG +V+K A + P + L + Sbjct: 143 -FNPSMLTMTVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKSAEEAPLAVLRV 201 Query: 193 VELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKV 252 V+L + IPAGV+++++G E G L + V+K++FTGS E G+ + + A+ + V Sbjct: 202 VQLINTV-IPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKIVYKTAAEKLIPV 260 Query: 253 SLELGGNAPFIVFDDADLDKAVEGAIIS-KYRNNGQTCVCANRIYVQDGVYDAFAEKLAA 311 +LELGG +P IV DADLD+A+ GAI ++ GQ+C ++RI+V D ++DAF EKL Sbjct: 261 TLELGGKSPMIVCGDADLDQAIAGAIAGMRFTRQGQSCTASSRIFVHDSIHDAFVEKLKE 320 Query: 312 AVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAK------VLSGGKLIEGNF 365 V +K+G+ L+E T G ++ + + +VQ +I GA + S KL +G + Sbjct: 321 KVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCSAMPSDPKLTKGLY 380 Query: 366 FEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVF 425 +P I V + +A+EE FGP+ + R+ D EVIA +NDTE+GLA+ + RD+ Sbjct: 381 VQPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGLAATIWTRDLKVAM 440 Query: 426 RVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGS 463 LE G V +N L+ +GG+K+SGLG+E S Sbjct: 441 DAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEAS 478 Lambda K H 0.317 0.134 0.384 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: 538 Number of extensions: 22 Number of successful extensions: 5 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: 480 Length of database: 497 Length adjustment: 34 Effective length of query: 446 Effective length of database: 463 Effective search space: 206498 Effective search space used: 206498 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 (21.6 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