Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate HSERO_RS05645 HSERO_RS05645 succinate-semialdehyde dehdyrogenase
Query= BRENDA::P51650 (523 letters) >FitnessBrowser__HerbieS:HSERO_RS05645 Length = 493 Score = 499 bits (1284), Expect = e-145 Identities = 249/485 (51%), Positives = 336/485 (69%), Gaps = 7/485 (1%) Query: 45 DLLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKE 102 DL+ G +G W V DPA+G +V D G +ARAAV AA AF++W+ Sbjct: 10 DLMPGAQLIGADWRGAADGRQLDVSDPATGQVFASVPDGGAADARAAVEAAVAAFAAWRA 69 Query: 103 ISVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRV 162 K+R+ ++++W DL++ ++D+L ++I+ E GKPL EA+GE+ Y+A ++EWF EEA R Sbjct: 70 TPAKQRAGIIKRWNDLLLAHQDDLGRLISREQGKPLAEAKGEVAYAASYVEWFGEEATRA 129 Query: 163 YGDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTP 222 GDII +R + LK+PVGV + ITPWNFP+AMI RK+ ALAAGCTVV KPAEDTP Sbjct: 130 NGDIIPAPVTGRRMMALKEPVGVVAAITPWNFPAAMIARKIAPALAAGCTVVCKPAEDTP 189 Query: 223 YSALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLH 282 ++LAL +LA +AG+P GV N++ SR + EV +V D V KISFTGSTA GK L Sbjct: 190 LTSLALVRLAQEAGVPVGVINIVTASRERTPEVVDVWLADGRVRKISFTGSTAVGKHLAR 249 Query: 283 HAANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHD 342 H+A+++K++S+ELGG APFIVFD A+VD A+ G MA+KFRN GQTCV NR VQ ++D Sbjct: 250 HSADTLKKLSLELGGNAPFIVFDDADVDAAIDGVMAAKFRNGGQTCVSPNRIYVQEKVYD 309 Query: 343 SFVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQ 402 +FV K A +L+VG + + GP+IN +A+ K+++HV DA+A+GA V+TGGKR Q Sbjct: 310 AFVDKLG-ARVAALKVGPATDPASQIGPMINARAIAKIDQHVRDAIARGARVITGGKRLQ 368 Query: 403 SGG----NFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYF 458 G N++ PT+L++VT M C EETFGPVAP+ +F E+E +A ANA GLA YF Sbjct: 369 GPGFGSDNYYAPTVLADVTGAMQCSCEETFGPVAPITRFATEDEVIAAANATPFGLAAYF 428 Query: 459 YSQDPAQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYV 518 YS D +I RV + LE G+VGVNEG +++ PFGGVK+SG GREGS +G+D+YL KYV Sbjct: 429 YSTDVRRIHRVTDALESGIVGVNEGALAAEAAPFGGVKESGYGREGSVHGLDDYLHTKYV 488 Query: 519 CYGGL 523 C G L Sbjct: 489 CQGQL 493 Lambda K H 0.318 0.135 0.400 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: 666 Number of extensions: 29 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: 523 Length of database: 493 Length adjustment: 34 Effective length of query: 489 Effective length of database: 459 Effective search space: 224451 Effective search space used: 224451 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