Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_009763662.1 MICLODRAFT_RS20175 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P51650 (523 letters) >NCBI__GCF_000262405.1:WP_009763662.1 Length = 495 Score = 521 bits (1342), Expect = e-152 Identities = 259/480 (53%), Positives = 346/480 (72%), Gaps = 6/480 (1%) Query: 46 LLRGDSFVGGRWLPTP--ATFPVYDPASGAKLGTVADCGVPEARAAVRAAYDAFSSWKEI 103 LL G ++V G W+ P T PV DP GA + V D G AR A+ A+ W + Sbjct: 20 LLVGQAYVAGEWIDAPDGKTIPVTDPFDGALILEVPDLGPDAARRAIDKAHAVQKDWAKR 79 Query: 104 SVKERSSLLRKWYDLMIQNKDELAKIITAESGKPLKEAQGEILYSAFFLEWFSEEARRVY 163 + KERS++LR+WYDL++ N D+LA I+T E GKPL EA+GE++ +A ++EWF+EEA+R+ Sbjct: 80 TAKERSAILRRWYDLIVANADDLALILTTEQGKPLAEAKGEVISNAAYIEWFAEEAKRID 139 Query: 164 GDIIYTSAKDKRGLVLKQPVGVASIITPWNFPSAMITRKVGAALAAGCTVVVKPAEDTPY 223 GD+I + +R +VLKQPVGV + ITPWNFP+ MITRKVG ALAAGCT+V+KPA TP Sbjct: 140 GDVIPGATPSQRIVVLKQPVGVCAAITPWNFPNGMITRKVGPALAAGCTMVLKPAAQTPL 199 Query: 224 SALALAQLANQAGIPPGVYNVIPCSRTKAKEVGEVLCTDPLVSKISFTGSTATGKILLHH 283 SALALA LA +AG+P G ++V+ +AK +GE C +P V+KI+FTGST G+ L+ Sbjct: 200 SALALAVLAERAGVPKGAFSVV---TGEAKPIGEEFCHNPKVAKITFTGSTGVGRWLMKE 256 Query: 284 AANSVKRVSMELGGLAPFIVFDSANVDQAVAGAMASKFRNAGQTCVCSNRFLVQRGIHDS 343 AA+ +KR+S+ELGG APFIVFD A++D AV GAMASKFRNAGQTCVC+NR VQ G+ ++ Sbjct: 257 AADGIKRLSLELGGNAPFIVFDDADLDAAVEGAMASKFRNAGQTCVCANRIYVQEGVAEA 316 Query: 344 FVTKFAEAMKKSLRVGNGFEEGTTQGPLINEKAVEKVEKHVNDAVAKGATVVTGGKRHQS 403 F K A A SL++G G + G T GPLI+++AV K+E+HV D + KG ++ GGKR Sbjct: 317 FAEKLA-AKAGSLKLGRGTDAGVTMGPLIDDRAVAKMEEHVRDVLDKGGKLLVGGKRSDL 375 Query: 404 GGNFFEPTLLSNVTRDMLCITEETFGPVAPVIKFDKEEEAVAIANAADVGLAGYFYSQDP 463 G FFEPT+++ VT+ M EETF P+AP+I F E + +A+AN ++ GLA YFY++D Sbjct: 376 GSTFFEPTVMTGVTQAMKVTKEETFAPLAPIITFKDEADVIAMANDSEFGLASYFYAKDM 435 Query: 464 AQIWRVAEQLEVGMVGVNEGLISSVECPFGGVKQSGLGREGSKYGIDEYLEVKYVCYGGL 523 A++WRVAE LE GMVGVN +++ PFGGVKQSGLGREGSKYGI+ +LE+KY+ GL Sbjct: 436 ARVWRVAEALESGMVGVNTPALANEMAPFGGVKQSGLGREGSKYGIEGFLEIKYINLAGL 495 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: 678 Number of extensions: 25 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: 495 Length adjustment: 34 Effective length of query: 489 Effective length of database: 461 Effective search space: 225429 Effective search space used: 225429 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 24 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