Align succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized)
to candidate WP_012470910.1 GLOV_RS14220 aldehyde dehydrogenase
Query= CharProtDB::CH_007085 (453 letters) >NCBI__GCF_000020385.1:WP_012470910.1 Length = 471 Score = 278 bits (710), Expect = 4e-79 Identities = 158/438 (36%), Positives = 245/438 (55%), Gaps = 4/438 (0%) Query: 10 LIEKAKVAQKKLEAYSQEQVDVLVKALGKVVYDNAEMFAKEAVEETEMGVYEDKVAKCHL 69 ++E+A+VA ++ +S + VD +V+A+ V + + +A+ V ET GV E K K Sbjct: 19 MLEQAQVAAREFAKFSPQAVDKIVEAVAAVAAERSAFYAEWIVRETGYGVVEHKTIKNEG 78 Query: 70 KSGAIWNHIKDKKTVGIIKEEPERALVYVAKPKGVVAATTPITNPVVTPMCNAMAAIKGR 129 S + N K + G + + E+ +V +A+P GVV A P TNPV T + ++ R Sbjct: 79 SSAGLVNFYKGQNFCGY-EIDTEKKVVKIARPAGVVLALVPSTNPVATTYYKILLSLMSR 137 Query: 130 NTIIVAPHPKAKKVSAHTVELMNAELKKLGAPENIIQIVEAPSREAAKELMESADV--VI 187 N +I+ PHP AK + + + A +K G P+ +IQ+V PS + +M+S V ++ Sbjct: 138 NAVILCPHPAAKGCIVGSADELTAVAEKAGLPKGVIQVVREPSIALLETMMKSDQVNLIL 197 Query: 188 ATGGAGRVKAAYSSGRPAYGVGPGNSQVIVDKGYDYNKAAQDIITGRKYDNGIICSSEQS 247 ATGG G V+AAYSSG PA GVGPGN VD +KAA DI +DN + C+S+ Sbjct: 198 ATGGPGVVRAAYSSGNPAIGVGPGNVGHYVDGTGSLDKAALDIAISSGFDNNLGCTSDSV 257 Query: 248 VIAPAEDYDKVIAAFVENGAFYVEDEETVEKFRSTLFKDGKINSKIIGKSVQIIADLAGV 307 + + D ++ A NG +ED++ +EK R+ L+ DG N IGKS IA+ AG+ Sbjct: 258 ALVERDVADAMLEALSRNGVLKLEDKDDIEKVRNVLYPDGGFNPAAIGKSAAWIANEAGI 317 Query: 308 KVPEGTKVIVLKGKGAGEKDVLCKEKMCPVLVALKYDTFEEAVEIAMANYMYEGAGHTAG 367 + E K++ ++ +KD+ +EK+ PVL L+ D + A A A GAGHTA Sbjct: 318 SINEDIKILCVEVDKIDDKDIYTREKLFPVLGFLRIDGLDAAYRAAEAMIAMGGAGHTAA 377 Query: 368 IHSDNDENIRYAGTVLPISRLVVNQPATTAGGSFNNGFNPTTTLGCGSWGRNSISENLTY 427 IHS + + I A + LP+ R+ N PA F +G PT T+G G +GR+S+ EN+ Sbjct: 378 IHSKDSDKI-VAWSQLPVYRIATNGPAPLVASGFASGLAPTMTVGTGFFGRSSVCENVGP 436 Query: 428 EHLINVSRIGYFNKEAKV 445 +HLI+ ++I Y + ++V Sbjct: 437 QHLIHWTQIAYSDDPSEV 454 Lambda K H 0.313 0.131 0.368 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: 523 Number of extensions: 27 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: 453 Length of database: 471 Length adjustment: 33 Effective length of query: 420 Effective length of database: 438 Effective search space: 183960 Effective search space used: 183960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 51 (24.3 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