Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate Echvi_3822 Echvi_3822 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::B1XMM6 (454 letters) >FitnessBrowser__Cola:Echvi_3822 Length = 453 Score = 433 bits (1114), Expect = e-126 Identities = 221/450 (49%), Positives = 297/450 (66%), Gaps = 1/450 (0%) Query: 5 TINPTTGEICQRFKALTPAEIDAKLAKAQEAFQAYRRTSFSQRRQWLENAAAILERDTSK 64 +INP TGE+ + F T +++A + K QEA+ ++R SQR ++ A +L +T K Sbjct: 3 SINPYTGELLEEFTDHTEQQVEAAIQKGQEAYLSWRELPISQRADLMKKAGQVLRDNTDK 62 Query: 65 FAEIMTTEMGKTHQSAIAEAEKSALVCRYYAEHGEQFLANE-YTETQATESYVCYQPLGI 123 + +I++ EMGK + +E EK A VC YYAE+ E+ LA+ E+ V Y PLGI Sbjct: 63 YGKIISLEMGKVITESKSEVEKCAWVCEYYAENAEEMLADAPIALPDGKEAKVVYNPLGI 122 Query: 124 LLAVMPWNFPFWQVFRFAAPALMAGNVAVLKHASNVPQCALAVEAILEAAGFPEGVFQTL 183 +LAVMPWNFPFWQVFRFAAP L AGNV +LKHASNVPQCALA+E + AGFPEGVFQ+L Sbjct: 123 VLAVMPWNFPFWQVFRFAAPNLTAGNVGLLKHASNVPQCALAIEEVFTQAGFPEGVFQSL 182 Query: 184 LIGASQVEQVIKDPRVKAATLTGSEPAGASLASLAGQEIKPTLLELGGSDPFVVFPSADL 243 LIG+ +V +I P VKAATLTGSE AG +A+ AG++IK T+LELGGSDPF+V AD+ Sbjct: 183 LIGSDKVANIIAHPDVKAATLTGSEKAGQKIAAQAGEQIKKTVLELGGSDPFIVLKDADV 242 Query: 244 DEAVEVGTVARTMNNGQSCIAAKRFILHEAIAAEFLEKLHLKFASLKIGDPMAPETDIGP 303 EA + R +N GQSCIAAKRFI+ + + EF+ S GDP+ + Sbjct: 243 KEAAKTAAKGRMINFGQSCIAAKRFIIEQEVYDEFITHFKSAIESYVPGDPLDEKAGYAC 302 Query: 304 LATEGILQDISRQVDQAVAAGAKILLGGRPLDRAGYFYPPTILTEIPPGAKILQEELFAP 363 +A + ++ QV+ ++ GA+++L G ++ F P IL ++ P +EELF P Sbjct: 303 MARPDLAMELYEQVEASIQKGAEVILEGTKPEKGKAFIKPYILGKLTPDMPAYREELFGP 362 Query: 364 VAMVFTVKDLDQAIALANDIPFGLGASAWTNDPAEQQRFIQELDAGAVFINGMVKSDPRL 423 VA VF D+D+AIA+AND FGLGAS WT DP + +++++GAVFIN MV S+P L Sbjct: 363 VASVFKANDVDEAIAIANDSAFGLGASLWTQDPQKADILSRKIESGAVFINSMVASNPYL 422 Query: 424 PFGGTKRSGYGRELGLAGIRTFVNAKTVWL 453 PFGG K+SGYGREL GI+ F+N KTV+L Sbjct: 423 PFGGIKKSGYGRELAENGIKEFMNIKTVYL 452 Lambda K H 0.319 0.134 0.389 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: 540 Number of extensions: 20 Number of successful extensions: 2 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: 454 Length of database: 453 Length adjustment: 33 Effective length of query: 421 Effective length of database: 420 Effective search space: 176820 Effective search space used: 176820 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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