Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate RR42_RS27350 RR42_RS27350 aldehyde dehydrogenase
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__Cup4G11:RR42_RS27350 Length = 486 Score = 408 bits (1048), Expect = e-118 Identities = 216/483 (44%), Positives = 305/483 (63%), Gaps = 3/483 (0%) Query: 4 ITEQNTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTA 63 + + + + N+INGEW KS SG NPAD DIVG Q STA+D + AV AA A A Sbjct: 3 VAKTDEFNNYINGEWSKSASGRTFDNVNPADTADIVGRFQASTADDAQAAVAAAAAAFDA 62 Query: 64 WRKLTGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKGETARGIAILRYYAGEG 123 W+K ++R + L AD +E E+IA TRE GK L +K E R +R+YA EG Sbjct: 63 WKKTPISKRAKILNGAADYLEANAEQIAEELTREEGKALNLSKDEVLRSAQTIRFYAVEG 122 Query: 124 MRKTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPAT 183 +G+ P D D ++++ R PLGVV VISPWNFPV+IP K+APAL+ GNTVV KP++ Sbjct: 123 QSFSGETYPQDDPDMIVYSQREPLGVVTVISPWNFPVSIPARKIAPALIAGNTVVFKPSS 182 Query: 184 ETAVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQ 243 + ++ ++ F EAG+P GV+N +TG VG + E V A++FTGS G+ I Sbjct: 183 DAPLSGYRLAQAFVEAGIPKGVLNFITGRAGDVGAAITEAPAVRAISFTGSTAAGQHI-H 241 Query: 244 AALARGAKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYE 303 +++ + Q+E+GGKNP+IV +DADL+ A + I G +GQ CT TSRV+V + + Sbjct: 242 RSVSLSTRTQMELGGKNPLIVMEDADLDRAVDLTIKGGLSLSGQACTGTSRVLVMASVKA 301 Query: 304 RFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLEN 363 + EKLL + K + IG + + +GP+A++ QL+ L Y+E GK E A+ L GG++L Sbjct: 302 AYTEKLLAKVKTLKIGSGMTPGMDVGPLATRKQLETVLGYVEAGKSE-ATHLCGGDRLGG 360 Query: 364 GKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIF 423 Y G+YV PA+F VT +M IA+EEIFGPVIA+I+V S +A+ AND ++GLSA+I Sbjct: 361 EPYDKGFYVSPAVFTGVTQQMRIAREEIFGPVIAIIEVSSYADAIAKANDTEYGLSAAIV 420 Query: 424 TENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHS-REQGEAAKDFFTAIK 482 T N F +I +G V+IN + G + APFGG+KQSS+ + RE G A +F+T IK Sbjct: 421 TSNPRYAHDFAHDIQSGTVKINRTTTGNLINAPFGGLKQSSTSTFRESGRAGLEFYTQIK 480 Query: 483 TVF 485 TV+ Sbjct: 481 TVY 483 Lambda K H 0.315 0.132 0.374 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: 570 Number of extensions: 26 Number of successful extensions: 4 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: 488 Length of database: 486 Length adjustment: 34 Effective length of query: 454 Effective length of database: 452 Effective search space: 205208 Effective search space used: 205208 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 (21.5 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