Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::C6KEM4 (506 letters) >FitnessBrowser__PV4:5211158 Length = 506 Score = 324 bits (831), Expect = 4e-93 Identities = 190/497 (38%), Positives = 279/497 (56%), Gaps = 21/497 (4%) Query: 13 FIGGAWREPCLGRRLPVVNPATEATIGDIPAGTAEDVEIAVAAARDAFSRDGGRQWSRAP 72 FIGG W P G +P + D+E+A+ AA A +D W + Sbjct: 22 FIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAA--KDA---WGKTS 76 Query: 73 GAVRANFLRAIAAKIKDRKSELALLETLDSGKPLDEA-SGDMDDVAACFEYYADLAEALD 131 R+N L IA +++ LA+ ET ++GK + E + D+ F Y+A A + Sbjct: 77 VTERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQE 136 Query: 132 GKQRSPISLPMENFKSYVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCTTILKPSEL 191 G + N SY EP+GVVG I PWN+PLLMA WK+APALAAG +LKP+E Sbjct: 137 GSAADIDN----NTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQ 192 Query: 192 ASVSCLELGAICMEIGLPPGVLNIITGLGPEAGAPLSSHSHVDKVAFTGSTETGKRIMTS 251 VS L + + ++ LP GVLNI+ G G EAG L+ + K+AFTGST+ G I+ Sbjct: 193 TPVSILVMVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHILKC 251 Query: 252 AAQMVKPVSLELGGKSPLIVFDDIGD-----IDKAVEWTMFGIFANAGQVCSATSRLLLH 306 AA+ + P ++ELGGKSP I F D+ + +DKAVE + F N G+VC+ SR+L+ Sbjct: 252 AAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLLAFF-NQGEVCTCPSRVLIA 310 Query: 307 EKIAKKFLDRLVAWAKNIKVSDPLEEGCRLGSVISEGQYEKIKKFISTARSEGATILYGG 366 E I KF+D+++A AK IK +PL+ ++G+ S+ Q++KI ++ R+EGA +L GG Sbjct: 311 ESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIGG 370 Query: 367 GRPQ---HLRRGFFLEPTIITDVSTSMQIWQEEVFGPVICVKEFRTDSEAVELANDTHYG 423 Q GF++EPTI+ M+++QEE+FGPVI V F+ ++EA+ +ANDT YG Sbjct: 371 TSCQLSGDQSSGFYIEPTILKG-HNKMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYG 429 Query: 424 LAGAVISNDQERCERISKALHSGIIWINCSQPCFVQAPWGGNKRSGFGRELGEWGLDNYL 483 L V + D R +R+ + + +G +WINC A +GG K+SG GRE + L +Y Sbjct: 430 LGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQ 489 Query: 484 TVKQVTKYCSDEPWGWY 500 K + P G++ Sbjct: 490 NTKNLLVSYDVNPLGFF 506 Lambda K H 0.318 0.136 0.418 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: 653 Number of extensions: 32 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: 506 Length of database: 506 Length adjustment: 34 Effective length of query: 472 Effective length of database: 472 Effective search space: 222784 Effective search space used: 222784 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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