Align 2-aminomuconate semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate GFF3202 HP15_3144 NAD-dependent aldehyde dehydrogenase
Query= metacyc::MONOMER-13349 (490 letters) >FitnessBrowser__Marino:GFF3202 Length = 533 Score = 330 bits (847), Expect = 6e-95 Identities = 180/482 (37%), Positives = 271/482 (56%), Gaps = 17/482 (3%) Query: 3 QYRNYINGEWVESARR--FDDVNPVDGTVVAQVHEADREAVDSAIRAGHAAVRGAWGRTT 60 +Y NYI GEWV + F+++ PV G V+ ++ + E +D A+ A H A AWG+T+ Sbjct: 45 RYENYIGGEWVAPVKGQYFENITPVTGNVICEIPRSSAEDIDLALDAAHKAAP-AWGKTS 103 Query: 61 VAERAAILCRIADEIDRRYDDFLAAEIADTGKPVAMASTIDIPRGAANFRVFADILKTAP 120 ER+ IL +IAD I+ + AE D GK V DIP A +FR FA L+ Sbjct: 104 PTERSNILLKIADRIEANLEKLAVAETWDNGKAVRETLNADIPLAADHFRYFAGCLRAQE 163 Query: 121 LDTFQTDLPDGARALNYAVRKPLGVVGVISPWNLPLLLLTWKIAPALACGNAVVAKPSEE 180 + D + Y +PLGVVG I PWN P+L+ WK+ P LA GN V KP+E+ Sbjct: 164 GHMGEID----HNTVAYHFHEPLGVVGQIIPWNFPILMAAWKLGPCLAAGNCTVLKPAEQ 219 Query: 181 TPGTATLLAEVMHTVGVPPGVFNLVHGFGPDSAGEFITTNDDIDAITFTGESRTGSAIMR 240 TP + +L E++ + +PPGV N+V+G+G + AG+ + T+ I I FTG + GS I++ Sbjct: 220 TPASILVLMEIIGDL-LPPGVLNIVNGYGIE-AGQALATSKRIAKIAFTGSTPVGSHILK 277 Query: 241 AAATHVKPVSFELGGKNAAIIFADCD------FEKMIDGMMRAVFLHSGQVCLCAERVYV 294 AA ++ P + ELGGK+ I F+D +K ++G++ A F + G+VC C R V Sbjct: 278 CAAENIIPSTVELGGKSPNIYFSDVMKAEPEFIDKCVEGLVLA-FFNQGEVCTCPSRALV 336 Query: 295 ERPIYNRFLDAFVERVKALKLGWPQDGTTGMGPLISAEHRDKVLSYFKLAREEGAQVLVG 354 + ++ F+ V+R K++K G P D +G S E DK++SY + +EEGA VL G Sbjct: 337 QEDMFEEFMQKVVQRTKSIKRGNPLDTDVQVGAQASKEQFDKIMSYLAIGKEEGAVVLTG 396 Query: 355 GGVPKFGDARDAGFWVEPTIITGLPQTARCIKEEVFGPICHVSPFDTEAEAIALANDTKY 414 G + + GF+++PT+ G R +EE+FGP+ V+ F TE EA+A+ANDT++ Sbjct: 397 GDREHLDEEFNNGFYIQPTLFKG-DNKMRVFQEEIFGPVVGVTTFKTEEEALAIANDTEF 455 Query: 415 GLSATTWTGNLNRGHRVSEAMRVGLSWVNSWFLRDLRTPFGGVGLSGIGREGGMHSLNFY 474 GL A WT + N +R+ ++ G W+N + FGG SG+GRE +L Y Sbjct: 456 GLGAGVWTRDTNLAYRMGRNIQAGRVWMNCYHAYPAHAAFGGYKKSGVGRETHKMALEHY 515 Query: 475 SE 476 + Sbjct: 516 QQ 517 Lambda K H 0.321 0.137 0.420 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: 639 Number of extensions: 24 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: 490 Length of database: 533 Length adjustment: 35 Effective length of query: 455 Effective length of database: 498 Effective search space: 226590 Effective search space used: 226590 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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