Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate RR42_RS05110 RR42_RS05110 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-13361 (500 letters) >FitnessBrowser__Cup4G11:RR42_RS05110 Length = 489 Score = 748 bits (1931), Expect = 0.0 Identities = 360/479 (75%), Positives = 414/479 (86%) Query: 22 NYIDGNFVTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRA 81 +YIDG FV SA +F + PV+G L+++V EADA V+ AV AA+ AL+GPWG+L VQ RA Sbjct: 11 HYIDGEFVASAGTFPDTCPVDGHLVANVCEADAALVDRAVQAARRALQGPWGQLDVQQRA 70 Query: 82 ALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFE 141 AL+H+IADGI+ARF+ FVAAEV DTGRP HQARTLD+ RA+ N RTFADLAKT+ +L+E Sbjct: 71 ALLHRIADGIEARFDAFVAAEVEDTGRPEHQARTLDVARAVTNLRTFADLAKTAGNELYE 130 Query: 142 MSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSA 201 T+DG+GALNYTVRKP+GV+G+ISPWNLPLLL TWKVAPALACGNTVVAKPSEE+P+SA Sbjct: 131 TPTADGAGALNYTVRKPVGVVGIISPWNLPLLLLTWKVAPALACGNTVVAKPSEETPASA 190 Query: 202 TLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADG 261 LLAEV+H AGVP GVFNL+HGFG S GEFLT+H GI A+TFTGES+TGSTIM+AVADG Sbjct: 191 ALLAEVIHQAGVPHGVFNLLHGFGGGSTGEFLTRHDGIDAITFTGESRTGSTIMRAVADG 250 Query: 262 VKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEFVSG 321 VKE+SFELGGKNAAVVFADAD DAA+ GVLRSSFTN+GQVCLCSERV+V R IFD FV+ Sbjct: 251 VKEISFELGGKNAAVVFADADFDAAVAGVLRSSFTNAGQVCLCSERVFVARPIFDAFVAA 310 Query: 322 LKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFNDERD 381 LK + L +G+P DGV+MGPLIS GHRDKV SY+RLAV+EGATVV GG VP F D RD Sbjct: 311 LKARTQALKLGHPGDDGVDMGPLISRGHRDKVESYFRLAVEEGATVVCGGKVPVFGDARD 370 Query: 382 QGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNL 441 GAYV PTIWTGL D ARCVTEEIFGPVCHI+PFD E+EVI RVNDS YGLACA+WTTNL Sbjct: 371 DGAYVMPTIWTGLPDSARCVTEEIFGPVCHIAPFDSEEEVIARVNDSAYGLACALWTTNL 430 Query: 442 SRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICIKI 500 +RAHRV+RQ+ VGL WVNTWYLRDLRTPFGGV LSGLGREGGR S+DFYS++ANICIK+ Sbjct: 431 TRAHRVARQVRVGLTWVNTWYLRDLRTPFGGVGLSGLGREGGRHSLDFYSEVANICIKL 489 Lambda K H 0.318 0.135 0.405 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: 791 Number of extensions: 19 Number of successful extensions: 1 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: 500 Length of database: 489 Length adjustment: 34 Effective length of query: 466 Effective length of database: 455 Effective search space: 212030 Effective search space used: 212030 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 (21.7 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