Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate Echvi_0535 Echvi_0535 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::Q64057 (539 letters) >FitnessBrowser__Cola:Echvi_0535 Length = 514 Score = 516 bits (1328), Expect = e-150 Identities = 268/503 (53%), Positives = 343/503 (68%), Gaps = 7/503 (1%) Query: 42 LQDLGLREDNEGVFNGSW--GGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAW 99 LQDLGL E N+G + G +GE +++Y P + + + +V+ + + YE+ + +A+KA+ Sbjct: 11 LQDLGLNEVNKGTWTGVEFIDIKGEWLSSYSPVDGKELGKVQMTTRESYEKVLDQAEKAF 70 Query: 100 NIWADIPAPKRGEIVRKIGDALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAG 159 W +PAP+RGE+VR+IG LR K LLG+LVS EMGK EG+GEVQE +D+CD+A G Sbjct: 71 KAWRKVPAPQRGEVVRQIGIELRNKKSLLGKLVSYEMGKSYQEGLGEVQEMIDICDFAVG 130 Query: 160 LSRMIGGPTLPSERPGHALMEQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKG 219 LSR + G T+ SERP H + EQW+PLG+VG+I+AFNFPVAV+ WN IA + G+VC+WK Sbjct: 131 LSRQLYGLTMHSERPSHRMYEQWHPLGIVGVISAFNFPVAVWSWNTMIAWVCGDVCVWKP 190 Query: 220 APTTSLVSIAVTKIIAKVLEDNLLPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVG 279 + T L S+A I A V N P I SL GGA++G + +D RV L+S TGSTQ+G Sbjct: 191 SEKTPLTSVACQLIAADVFNRNGFPEGITSLLIGGANVGAFLTQDPRVALISATGSTQMG 250 Query: 280 KQVALMVQERFGKSLLELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLH 339 K V V R GK LLELGGNNAII E ADL + + ALF AVGTAGQRCT+ RRL +H Sbjct: 251 KSVGETVGGRLGKVLLELGGNNAIIITEHADLDIAIRGALFGAVGTAGQRCTSTRRLIIH 310 Query: 340 ESIHDEVVDRLKNAYSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGG 399 ES+ +EV +R+ AYS++ +GNP D + + GPL K AV ++ A+E K EGG V G Sbjct: 311 ESVFEEVKERMVAAYSKLTIGNPLDEDNIVGPLIDKDAVQNYLTAIERVKAEGGKEVVAG 370 Query: 400 KVMDH----PGNYVEPTIVTGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGL 455 +++ G YV P++ H IV KETF PILY+ K+ +E N V QGL Sbjct: 371 GLLEGEEYVSGCYVRPSVFEAENH-FQIVQKETFGPILYLMKYSEFDEAIAMQNNVPQGL 429 Query: 456 SSSIFTKDLGRIFRWLGPKGSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQ 515 SS+I T ++ R+L +GSDCGI NVNI TSGAEIGGAFGGEK TGGGRESGSDAWK Sbjct: 430 SSAIMTTNMREAERYLSSEGSDCGISNVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKA 489 Query: 516 YMRRSTCTINYSTALPLAQGIKF 538 YMRR T TINYST LPLAQGIKF Sbjct: 490 YMRRQTNTINYSTDLPLAQGIKF 512 Lambda K H 0.319 0.137 0.417 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: 849 Number of extensions: 46 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: 539 Length of database: 514 Length adjustment: 35 Effective length of query: 504 Effective length of database: 479 Effective search space: 241416 Effective search space used: 241416 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 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