Align 2-deoxy-3-keto-D-ribonoate cleavage enzyme (characterized)
to candidate RR42_RS24450 RR42_RS24450 3-keto-5-aminohexanoate cleavage protein
Query= reanno::WCS417:GFF1426 (310 letters) >FitnessBrowser__Cup4G11:RR42_RS24450 Length = 310 Score = 405 bits (1042), Expect = e-118 Identities = 195/310 (62%), Positives = 237/310 (76%) Query: 1 MSKNRPVIITCAVTGAIHTPSMSPHLPITAQEIADAAIGAAEAGAAIVHLHARDPNDGRP 60 M + VII+CAVTGAIHTPSMSPHLPIT +EIA+++I AAEAGAAI+HLHARDP GRP Sbjct: 1 MYQQSKVIISCAVTGAIHTPSMSPHLPITPEEIAESSIAAAEAGAAIIHLHARDPVTGRP 60 Query: 61 SQDPALFAEFLPQIKAASDVVINITTGGAPTMGVEERLQPVMQFKPELASLNMGSMNFGL 120 Q P F F+ +IKA DVV+N+TTGG+P M V+ER+ P KPE+AS+N+GSMNFGL Sbjct: 61 DQRPEAFLPFVREIKARCDVVLNLTTGGSPYMTVQERMMPAKVLKPEIASMNVGSMNFGL 120 Query: 121 YEMLNRFTDFKHDWERPYLEESDDRIFRNTFRDITHILNACAENRTRFEIECYDIGHLYT 180 Y ML R+ +FKHDWE YLE S D IFRNTF D+ +L + N TR+E ECYD HLY Sbjct: 121 YPMLKRYKEFKHDWEHSYLESSKDLIFRNTFGDLQTVLTELSPNGTRYEFECYDTSHLYN 180 Query: 181 AAHFLERGLLKPPLFIQSVFGLRGGIGGHPEDLAHMRRTADRLFGSDYVWSILGAGRGQI 240 AH +E GL+K P FIQ+VFG+ GGIG HP+D+ HM+RTADRLFGSDY WS+LGAG Q+ Sbjct: 181 LAHLVELGLVKAPYFIQTVFGILGGIGTHPDDVMHMKRTADRLFGSDYRWSVLGAGASQM 240 Query: 241 PLATMGLSMGSNARVGLEDSLWDGPGKLAASNADQVRRIRTVIEALGHRVATPDEAREIL 300 +A M SMG+N RVGLED+LW G GKLA SNA+QV ++R +++ LG VA+P EAREIL Sbjct: 241 KIAGMAASMGANVRVGLEDNLWIGKGKLAQSNAEQVLKVREILDGLGLEVASPSEAREIL 300 Query: 301 GLKGRDQVNF 310 LKG QV F Sbjct: 301 QLKGASQVAF 310 Lambda K H 0.321 0.138 0.416 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: 333 Number of extensions: 6 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: 310 Length of database: 310 Length adjustment: 27 Effective length of query: 283 Effective length of database: 283 Effective search space: 80089 Effective search space used: 80089 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 (21.9 bits) S2: 48 (23.1 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