Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::B6ECN9 (505 letters) >FitnessBrowser__SB2B:6939342 Length = 506 Score = 324 bits (831), Expect = 4e-93 Identities = 188/484 (38%), Positives = 281/484 (58%), Gaps = 22/484 (4%) Query: 14 FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73 FI G+W P+ ++P + ++ + D+++A+ AA +A +D WG T+ + Sbjct: 22 FIGGKWVPPVGGEYFDNVSPVDGKVFCQAARSDYRDIELALDAAHAA--KDSWGKTSVTE 79 Query: 74 RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEAAS-DIDDVVACFEYYADLAEALDSKK 132 R+ L IA +V + LA +ET +NGK E + D+ V F Y+A A + Sbjct: 80 RSNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEG-- 137 Query: 133 QTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSELASI 192 + L ++ H L EPLGVVG I PWN+PLLM WK+APALAAG +LKP+E Sbjct: 138 -SAADLDANTVSYH-LPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPA 195 Query: 193 TSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMTAAAQ 252 + + L E ++ LPPG L+++ G G EAG+ L + + K+AFTGS G I+ AA+ Sbjct: 196 SIMVLLETIEDL-LPPGVLNVVNGFGAEAGAALATSKRIAKLAFTGSTEVGNHILKCAAE 254 Query: 253 LVKPVTLELGGKSPIVVFDDIHN-----LDTAVEWTLFGCFWTNGQICSATSRLIIQETI 307 + P T+ELGGKSP + F D+ N LD A+E L F+ G++C+ SR+++QE+I Sbjct: 255 NLIPSTVELGGKSPNIYFADVMNHEDNYLDKAIEGMLLA-FFNQGEVCTCPSRVLVQESI 313 Query: 308 APQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYGG--- 364 F+ +++ K I+ PL+ D ++G SR QY+KIL ++ + EGA +L GG Sbjct: 314 YDAFIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIGRAEGAKVLMGGEFK 373 Query: 365 --DRPEHLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKFGL 422 D PE K GYYIQPTI+ M +++EE+FGPV+ V TFK E EA+ +ANDT++GL Sbjct: 374 LQDGPE--KGGYYIQPTILKG-HNKMRVFQEEIFGPVVSVTTFKDEAEALAIANDTQYGL 430 Query: 423 GAAILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENYLN 482 GA + ++D+ +R + Q+G VWINC +GG K+SG GRE + L +Y N Sbjct: 431 GAGVWTRDMNLAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQN 490 Query: 483 IKQV 486 K + Sbjct: 491 TKNL 494 Lambda K H 0.318 0.136 0.421 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: 652 Number of extensions: 28 Number of successful extensions: 7 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: 505 Length of database: 506 Length adjustment: 34 Effective length of query: 471 Effective length of database: 472 Effective search space: 222312 Effective search space used: 222312 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