Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_015820919.1 TERTU_RS10425 succinylglutamate-semialdehyde dehydrogenase
Query= BRENDA::P76217 (492 letters) >NCBI__GCF_000023025.1:WP_015820919.1 Length = 480 Score = 458 bits (1179), Expect = e-133 Identities = 243/490 (49%), Positives = 319/490 (65%), Gaps = 13/490 (2%) Query: 2 TLWINGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAER 61 +++I+G W G G P +G+ LW+G+ A A V QA +A+ AF W + ER Sbjct: 3 SVFIDGLWREGCGEPIRSIEPATGKTLWEGHSASTADVFQAVESAQVAFKPWRNMPLTER 62 Query: 62 HAVVERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRS 121 +VV+ FA L S + EL II+RETGKP WE+ EVTAMINK+ ISI A R G R Sbjct: 63 TSVVKHFAECLLSRQQELAEIISRETGKPHWESLQEVTAMINKVDISISAQQQRAGTTR- 121 Query: 122 EMPDGAASLRHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGEAVM 181 D +L HRPHGV+AVFGPYNFPGHLPNGHIVPALLAGNT++FKPSE TP++ + + Sbjct: 122 ---DAQLALTHRPHGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEKTPYTAQRTL 178 Query: 182 RLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILA 241 +W QAGLP GV+NL+QGG G+ L D++G+LFTGS TG ++HR L+G PE +LA Sbjct: 179 EIWAQAGLPAGVINLIQGGASVGKTLID-SDINGVLFTGSHATGVKIHRALAGHPEILLA 237 Query: 242 LEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAV 301 LE+GGNNPLI+DEV +ID A I+SAF++ GQRCTCARRL+L G G+ L R++ Sbjct: 238 LELGGNNPLIVDEVDNIDVAAWHVIRSAFISTGQRCTCARRLVL-IGNTGERVLERVIQW 296 Query: 302 SQRLTPGNWDDEPQPFIGGLISEQAAQQVVTAWQQLEAMGGRPLLAPRLLQAGT-SLLTP 360 +L G+W D PF G LI A QQV+ +L A GG +L Q G + ++P Sbjct: 297 VPKLAIGHWQD--NPFFGPLIDTMAVQQVLKIQDKLIAAGGEAIL---FAQPGEHAFISP 351 Query: 361 GIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPEREKFDQLLL 420 GI+ + G V D+EVFGPLL+V+R + F +A+ +AN+TRFGL+ GL+S + L Sbjct: 352 GIVRINGNKTVFDDEVFGPLLQVYRAENFTQAVALANDTRFGLAAGLLSDNKAHQHIFLN 411 Query: 421 EARAGIVNWNKPLTGAASTAPFGGIGASGNHRPSAWYAADYCAWPMASLESDSLTLPATL 480 E+ AG+++ N+P GA+S PFGG G SGNHRPSA YAADY AWP + + T Sbjct: 412 ESNAGVISINQPTAGASSKLPFGGTGHSGNHRPSALYAADYSAWPQSQMLGGD-TAAQEP 470 Query: 481 NPGLDFSDEV 490 NP FS + Sbjct: 471 NPPQGFSANI 480 Lambda K H 0.318 0.134 0.412 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: 742 Number of extensions: 37 Number of successful extensions: 6 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: 492 Length of database: 480 Length adjustment: 34 Effective length of query: 458 Effective length of database: 446 Effective search space: 204268 Effective search space used: 204268 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 (21.7 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