Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_4383 (497 letters) >FitnessBrowser__HerbieS:HSERO_RS05115 Length = 793 Score = 317 bits (813), Expect = 8e-91 Identities = 188/462 (40%), Positives = 268/462 (58%), Gaps = 31/462 (6%) Query: 23 FINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSK 82 FI G +T + D + P G+LL ++ AD AV+ A+A W L Sbjct: 36 FIAGRFTQPKAD--LDDIDPASGKLLAHLSQGSAADVDAAVQAAQAALPG--WQALGGHG 91 Query: 83 RKATMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQAL----SWSGEAIDKL 138 R + A +++HA LA+LETLD GKP+ +S ++DVP A+ W+ + Sbjct: 92 RARHLYALARTVQRHARLLAVLETLDNGKPLRESRDVDVPLVARHFYHYAGWAQLQESEF 151 Query: 139 YDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPL 198 D V PVGVVG IVPWNFPL+M WK+ PAL+ GN+VVLKP+E + L Sbjct: 152 PDHV--------------PVGVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAENTSL 197 Query: 199 TALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGE 258 TAL A LA +AG+P GVLN++ G G T G A+ H + + FTGST++ + + + Sbjct: 198 TALLFAELAQQAGLPAGVLNIVTGDGAT-GAAVVAHPGIQKIAFTGSTEVGRLIREQTAG 256 Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSIKDTF 318 S K + LE GGKSP IVF DA D+ AA E AI FNQG+VC AGSRLLV+ I D F Sbjct: 257 SG-KSLTLELGGKSPFIVFEDA-DIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIHDLF 314 Query: 319 LPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRILEET 378 + + ++ K G PLD +++GAL+ Q+ V S +E G +GA+ +++ +T Sbjct: 315 IARLKTRMQKLKVGAPLDKCSDMGALISPVQLERVRSLVEQGVREGAQC----HQVVLDT 370 Query: 379 --GGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVWTK 436 GG + PT+ GV A +A EEIFGPVL ++F T ++A+++AN++ YGLAA++W++ Sbjct: 371 PPGGCFYPPTLLTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSE 430 Query: 437 DISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRD 478 I A A L+AG VW+N + D FGG ++SG GR+ Sbjct: 431 TIGLALGVAPQLKAGVVWINSTNQFDAAVGFGGVRESGYGRE 472 Score = 76.6 bits (187), Expect = 3e-18 Identities = 62/236 (26%), Positives = 100/236 (42%), Gaps = 5/236 (2%) Query: 34 GETFDCLSPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPSKRKATMIRFAGL 93 GE G L + + D + AV A +G W+ +P +R + A Sbjct: 531 GEVSMACHSTQGERLEDVGLGNRKDIRNAVA---AAVKAGGWTSASPHRRAQGLYYIAEN 587 Query: 94 LKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSWSGEAIDKLYDEVAATPHDQLGLV 153 L EE A G +D +V + + L G DK V P + L Sbjct: 588 LSARTEEFARRIASTTGVT-ADEARAEVDASIKRLFTYGAWADKFEGAVHQPPMRGVALA 646 Query: 154 TREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSEKSPLTALRIAALAIEAGIP 213 E +GVVG + P PL+ + P ++ GN VV+ PSE++PL A + + + +P Sbjct: 647 MPEAIGVVGVVCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVATDLYQVLDTSDLP 706 Query: 214 KGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYSGESNMKRIWLEAG 269 GV+N++ G + LA H +V+ L G + + S N+KR +++ G Sbjct: 707 AGVINIVTGKSAELLPVLAEHDEVEALWVRGPAEFSATAERLS-TGNLKRCFVDHG 761 Lambda K H 0.316 0.132 0.389 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: 978 Number of extensions: 49 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 497 Length of database: 793 Length adjustment: 38 Effective length of query: 459 Effective length of database: 755 Effective search space: 346545 Effective search space used: 346545 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 (21.6 bits) S2: 54 (25.4 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