Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= BRENDA::B6ECN9 (505 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 327 bits (838), Expect = 6e-94 Identities = 199/486 (40%), Positives = 283/486 (58%), Gaps = 26/486 (5%) Query: 14 FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73 +I G++ P+K I+P + ++ +T+ED+++AV AA A + W T+ + Sbjct: 17 YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKT--WSKTSSTE 74 Query: 74 RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEA-ASDIDDVVACFEYYADLAEA----L 128 R+ L IA ++ + LA +ETIDNGK E A+D+ V F Y+A + A L Sbjct: 75 RSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSL 134 Query: 129 DSKKQTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSE 188 Q V L ++ EP+GVV I PWN+PLLM WK+APALAAG +LKP+E Sbjct: 135 SELDQNTVSL--------IVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAE 186 Query: 189 LASITSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMT 248 ++ + L E+ ++ LPPG ++++ G G E G LV++P V K AFTGS PTG +M Sbjct: 187 STPVSIMVLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQ 245 Query: 249 AAAQLVKPVTLELGGKSPIVVF-----DDIHNLDTAVEWTLFGCFWTNGQICSATSRLII 303 A + + PVTLELGGKSP + F +D LD AVE + G+IC+ SRL+I Sbjct: 246 YATENIIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFAL-NQGEICTCPSRLLI 304 Query: 304 QETIAPQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYG 363 QE I +F+A+++E TK IKI PL+ +G S+ Q+EKI +I K+EGA +L G Sbjct: 305 QEDIYEKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTG 364 Query: 364 G---DRPEHLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKF 420 G + P L GYYI+PTI M I++EE+FGPVL V TFKT EEAIE+ANDT + Sbjct: 365 GEINELPGELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLY 423 Query: 421 GLGAAILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENY 480 GLGA + ++D + +A Q+G VW+N P+GG K+SG GRE + L +Y Sbjct: 424 GLGAGVWTRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHY 483 Query: 481 LNIKQV 486 K + Sbjct: 484 RQTKNM 489 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: 624 Number of extensions: 31 Number of successful extensions: 8 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: 501 Length adjustment: 34 Effective length of query: 471 Effective length of database: 467 Effective search space: 219957 Effective search space used: 219957 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