Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase
Query= BRENDA::A0A0E3T552 (503 letters) >FitnessBrowser__HerbieS:HSERO_RS09465 Length = 506 Score = 320 bits (821), Expect = 6e-92 Identities = 195/497 (39%), Positives = 280/497 (56%), Gaps = 22/497 (4%) Query: 11 FIDGEWREPVLKKRIPIINPATEEIIGHIPAATAEDVELAVEAARRALSRNKGRDWASAP 70 FI G++ PV + I+P + ++AEDVELA++AA A + W Sbjct: 22 FIGGKFVPPVKGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAAK-----KSWGKTS 76 Query: 71 GAVRAKYLRAIAAKIGERKPEIAKLEAIDCGKPLDEAAWDIDDVSGCFEYYAELAEGLDA 130 RA L IA ++ +A E +D GKP+ E D+ +++ A + Sbjct: 77 PTERANMLLKIADRMEANLELLATAETLDNGKPIRETM--AADIPLAIDHFRYFAAAVRT 134 Query: 131 QQKAPISLPMEQFKSHVLKEPIGVVGLITPWNYPLLMATWKVAPALAAGCAAILKPSELA 190 Q+ + + + + H EP+GVVG I PWN+P+LMA WK+APALAAG +LKP+E Sbjct: 135 QEGSICPIDNDTYAYH-FHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQT 193 Query: 191 SVTCLELADVCREVGLPPGVLNILTGLGHEAGAPLVSHPHVDKIAFTGSTMTGSKIMTAA 250 + + L ++ ++ +PPGV+NI+ G G EAG PL S+ + KIAFTG T TG IM A Sbjct: 194 PASIMVLIELIADL-IPPGVVNIVQGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYA 252 Query: 251 AQLVKPVSLELGGKSPIVVF------DDVDIDKAAEWTAFGCFWTN-GQICSATSRLILH 303 +Q + PV+LELGGKSP + F DD DKA E F F N G++C+ SR+++ Sbjct: 253 SQNLIPVTLELGGKSPNIFFADVLDKDDDFFDKALE--GFAMFALNQGEVCTCPSRVLVQ 310 Query: 304 ENIATEFLDRLLKWCKNIKIADPLEEGCRLGPVVSGGQYEKILKSIETAKSEGARVLSGG 363 E+I F++R LK IK +PL++ +G S Q EKIL I+ K EGA+VL+GG Sbjct: 311 ESIYERFIERALKRVAAIKQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEGAKVLAGG 370 Query: 364 DRPE---HLKKGFFIEPTIITDVTTSMQIWREEVFGPVLCVKTFSSEDEALELANDTHYG 420 R E L G++++PT+ M+I++EE+FGPV+ V TF E+EAL +ANDT YG Sbjct: 371 GREELGGDLASGYYVKPTVFQG-NNKMRIFQEEIFGPVVSVTTFKDEEEALAIANDTLYG 429 Query: 421 LGAAVISKDLERCDRFSKGLQAGIVWINCSQPCFCQAPWGGNKRSGFGRELGKWGLDNYL 480 LGA + ++D R R + +QAG VW NC A +GG K+SG GRE K LD+Y Sbjct: 430 LGAGLWTRDGTRAFRMGREIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQ 489 Query: 481 TVKQVTEYVSDDPWGWY 497 K + S G++ Sbjct: 490 QTKNLLVSYSPKALGFF 506 Lambda K H 0.319 0.136 0.424 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: 640 Number of extensions: 31 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: 503 Length of database: 506 Length adjustment: 34 Effective length of query: 469 Effective length of database: 472 Effective search space: 221368 Effective search space used: 221368 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