Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase
Query= BRENDA::P77674 (474 letters) >FitnessBrowser__HerbieS:HSERO_RS09465 Length = 506 Score = 318 bits (814), Expect = 3e-91 Identities = 180/472 (38%), Positives = 265/472 (56%), Gaps = 17/472 (3%) Query: 15 EGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTTPKVRAECLLKLADVI 74 +GE +P G E+A +SAE V+ A+ AA AA WG+T+P RA LLK+AD + Sbjct: 32 KGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAAKKSWGKTSPTERANMLLKIADRM 91 Query: 75 EENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLNGLAAGEYLEGHTSMI 134 E N ++ A E+ + GKP+ +IP +D FR+FA A R G ++ T Sbjct: 92 EANLELLATAETLDNGKPIRETMAADIPLAIDHFRYFAAAVRTQEGSICP--IDNDTYAY 149 Query: 135 R-RDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPLTALKLAELAKDIFP 193 +PLGVV I PWN+P++MA WKLAPALAAGNCVVLKP+E TP + + L EL D+ P Sbjct: 150 HFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPASIMVLIELIADLIP 209 Query: 194 AGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTASSIKRTHMELGGKAPV 253 GV+NI+ G G G PL + ++ ++ TG TG I+ + + ++ +ELGGK+P Sbjct: 210 PGVVNIVQGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYASQNLIPVTLELGGKSPN 269 Query: 254 IVF------DDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVEKLGAAVATL 307 I F DD + +EG F N G+ CT R+ Q+ IY+ +E+ VA + Sbjct: 270 IFFADVLDKDDDFFDKALEGFAMFA-LNQGEVCTCPSRVLVQESIYERFIERALKRVAAI 328 Query: 308 KSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRK-----GNGYYYAP 362 K G P D+ST +G +S LE++ ++ K G KV+ GG + + +GYY P Sbjct: 329 KQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEG-AKVLAGGGREELGGDLASGYYVKP 387 Query: 363 TLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRAHRVS 422 T+ G I Q+E+FGPVVSVT F +EE+ + AND+ YGL + +WT+D RA R+ Sbjct: 388 TVFQGN-NKMRIFQEEIFGPVVSVTTFKDEEEALAIANDTLYGLGAGLWTRDGTRAFRMG 446 Query: 423 ARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVKH 474 +Q G W N + + + GG K SG G++ L+ Y ++++V + Sbjct: 447 REIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKNLLVSY 498 Lambda K H 0.317 0.134 0.397 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: 23 Number of successful extensions: 4 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: 474 Length of database: 506 Length adjustment: 34 Effective length of query: 440 Effective length of database: 472 Effective search space: 207680 Effective search space used: 207680 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