Align succinate-semialdehyde dehydrogenase [NAD(P)+]; EC 1.2.1.16 (characterized)
to candidate WP_015942717.1 DHAF_RS01855 acetaldehyde dehydrogenase
Query= CharProtDB::CH_007085 (453 letters) >NCBI__GCF_000021925.1:WP_015942717.1 Length = 495 Score = 312 bits (799), Expect = 2e-89 Identities = 166/445 (37%), Positives = 261/445 (58%), Gaps = 6/445 (1%) Query: 8 KELIEKAKVAQKKLEAYSQEQVDVLVKALGKVVYDNAEMFAKEAVEETEMGVYEDKVAKC 67 + L++KAK AQ L ++++Q+D ++ ++ V +NAE A+ A +ETE G+ E K+AK Sbjct: 14 RNLVQKAKEAQLHLAHFNEQQIDKILASIVAAVEENAEGLARMACQETEYGIVEHKIAKN 73 Query: 68 HLKSGAIWNHIKDKKTVGIIKEEPERALVYVAKPKGVVAATTPITNPVVTPMCNAMAAIK 127 + ++ K KT+G I E+P+R ++ A P GV+ TP TNP T + NA+ AIK Sbjct: 74 LFAARDVYESTKHIKTIGTISEDPDRKVIRYAAPMGVLVGITPRTNPTSTIIHNALCAIK 133 Query: 128 GRNTIIVAPHPKAKKVSAHTVELMNAELKKLGAPENIIQIVEAPSREAAKELMESADV-- 185 G N I+ +PHP A + T L+N K GAP+ + + S +A+ ELM DV Sbjct: 134 GANAIVFSPHPFAVQCGCATASLINEAAVKAGAPDGVCSCLSMTSLQASHELMHHPDVAA 193 Query: 186 VIATGGAGRVKAAYSSGRPAYGVGPGNSQVIVDKGYDYNKAAQDIITGRKYDNGIICSSE 245 +IATGG G VK+AYS+G+PA+GVG GN V +++ D +A DI+ + +DNG+IC+SE Sbjct: 194 IIATGGPGLVKSAYSAGKPAFGVGSGNVPVFIERSADIKQAVNDIMVSKTFDNGMICASE 253 Query: 246 QSVIAPAEDYDKVIAAFVENGAFYVEDEETVEKFRSTLFKDGKINSKIIGKSVQIIADLA 305 Q+++A D+VI GA+++ EE + R + +G +N+ ++G+S +IA A Sbjct: 254 QAILADQPIKDEVIKELQNQGAYFLSPEEVQKVGRVVIHANGSMNNALVGQSPAVIAQRA 313 Query: 306 GVKVPEGTKVIVLKGKGAGEKDVLCKEKMCPVLVALKYDTFEEAVEIAMANYMYEGAGHT 365 G+ +P T +++ +G G+ L EK+ VL ++EA +++ G GH+ Sbjct: 314 GISIPADTALLIAPMEGYGKDYPLSHEKLTTVLGFYVVQDWKEACHLSIELLKLGGIGHS 373 Query: 366 AGIHSDNDENIRYAGTVLPISRLVVNQPATTAGGSFNNGFNPTTTLGCGSWGRNSISENL 425 IHS N++ IR P+ R++VN P+ G G P+ TLGCG+WG +SISENL Sbjct: 374 CAIHSQNEQVIR-EFLAKPVFRIIVNTPSALGGIGQTTGIMPSLTLGCGTWGGSSISENL 432 Query: 426 TYEHLINVSRIGYFNKEA---KVPS 447 +HLIN+ + Y K+ KVP+ Sbjct: 433 GPQHLINIKHLTYGLKKVAFHKVPA 457 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: 563 Number of extensions: 38 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: 495 Length adjustment: 33 Effective length of query: 420 Effective length of database: 462 Effective search space: 194040 Effective search space used: 194040 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