Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate GFF2231 Psest_2276 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::B6ECN9 (505 letters) >FitnessBrowser__psRCH2:GFF2231 Length = 506 Score = 325 bits (834), Expect = 2e-93 Identities = 192/481 (39%), Positives = 276/481 (57%), Gaps = 16/481 (3%) Query: 14 FIDGEWREPLKKNRLPIINPANEEIIGYIPAATEEDVDMAVKAARSALRRDDWGSTTGAQ 73 +I GE+ P+K +P N E+I P + ED++ A+ AA +A D WG T+ Sbjct: 22 YIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEKALDAAHAAA--DAWGKTSVQD 79 Query: 74 RAKYLRAIAAKVLEKKPELATLETIDNGKPWFEAAS-DIDDVVACFEYYADLAEALDSKK 132 RA L IA ++ +LA ET DNGK E + D+ F Y+A A + Sbjct: 80 RALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGSA 139 Query: 133 QTEVKLHLDSFKTHVLREPLGVVGLITPWNYPLLMTTWKVAPALAAGCAAILKPSELASI 192 E+ H ++ H EPLGVVG I PWN+PLLM WK+APALAAG +LKP+E + Sbjct: 140 -AEINEHTAAYHFH---EPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTPL 195 Query: 193 TSLELGEICREVGLPPGALSILTGLGHEAGSPLVSHPDVDKIAFTGSGPTGVKIMTAAAQ 252 + + E+ ++ LPPG L+I+ G G EAG L + + KIAFTGS P G IM AA+ Sbjct: 196 SIMVFIEVVGDL-LPPGVLNIVQGFGREAGQALATSTRIAKIAFTGSTPVGSHIMRCAAE 254 Query: 253 LVKPVTLELGGKSPIVVFDDIHNLDTA-VEWTLFG---CFWTNGQICSATSRLIIQETIA 308 + P T+ELGGKSP + F+DI N + A +E G F+ G++C+ SR +IQE+I Sbjct: 255 NIIPSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEVCTCPSRALIQESIF 314 Query: 309 PQFLARLLEWTKNIKISDPLEEDCKLGPVISRGQYEKILKFISTAKDEGATILYGGDRPE 368 F+ +++ K IK +PL+ D +G S Q++KIL ++ A+ EGA IL GG + Sbjct: 315 EPFMEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQQEGAQILTGGAAEK 374 Query: 369 ---HLKKGYYIQPTIITDVDTSMEIWKEEVFGPVLCVKTFKTEEEAIELANDTKFGLGAA 425 L GYY+QPT+I M +++EE+FGPV+ V TFK E EA+ +ANDT+FGLGA Sbjct: 375 LEGSLSTGYYVQPTLIKG-HNKMRVFQEEIFGPVVGVATFKDEAEALAIANDTEFGLGAG 433 Query: 426 ILSKDLERCERFTKAFQSGIVWINCSQPCFWQPPWGGKKRSGFGRELGEWSLENYLNIKQ 485 + ++D+ R R + ++G VW NC +GG K+SG GRE + L++Y K Sbjct: 434 VWTRDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKN 493 Query: 486 V 486 + Sbjct: 494 L 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: 594 Number of extensions: 26 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: 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