Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB
Query= SwissProt::P42236 (488 letters) >FitnessBrowser__Phaeo:GFF2135 Length = 485 Score = 325 bits (834), Expect = 2e-93 Identities = 189/478 (39%), Positives = 285/478 (59%), Gaps = 13/478 (2%) Query: 12 NFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEAKTAWRKLTGAE 71 +FINGE+V+ +G + V A + + V +T VE+A++ A A+ AW ++TG E Sbjct: 11 HFINGEYVEDTAGTPIPVIYAA-TGEQIATVHAATPAIVEQALSTAKAAQKAWARMTGTE 69 Query: 72 RGQYLYKTADIMEQRLEEIAACATREMGKTLPEAK-GETARGIAILRYYAGEGMRKTGDV 130 RG+ L + ADIM +R +++ T + GK L E + G L Y+ G TG+ Sbjct: 70 RGRILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTGEH 129 Query: 131 IPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVIKPATETAVTCA 190 IP + ++T R LG+ I WN+P I WK APAL GN++V KP+ T + Sbjct: 130 IPLGED--WVYTKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCAL 187 Query: 191 KIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGKIIGQAALARGA 250 K+ EAG PAGV N+V G G V G L V+ V+ TGS GK + AA A G Sbjct: 188 KVAEILIEAGAPAGVFNVVQGMGEV-GGALVTDPRVDKVSLTGSVPTGKKV-YAAAAEGM 245 Query: 251 KY-QLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQSGIYERFKEKL 309 K+ +E+GGK+P+I+ DDAD++ A I G F S+GQ C+ +RV VQ GI E+F +L Sbjct: 246 KHVTMELGGKSPLIIFDDADIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARL 305 Query: 310 LQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGGEKLENGKYQNG 369 +RT + +GD + E GP+ ++NQ++ L YIEKGK+EGA L+ GG + + +G Sbjct: 306 AERTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGRRAD----MDG 361 Query: 370 YYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGLSASIFTENIGR 429 Y+++P +F +VT +MTIA+EEIFGPV++++ D+ EE + AND +FGLSA +FT++ R Sbjct: 362 YFIEPTVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTR 421 Query: 430 MLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFFTAIKTVFVK 487 I ++AG IN+ + ++APFGG+K +S RE + A F+ +K+V+V+ Sbjct: 422 AHRVIGNLEAGSCFINSYN-DAPVEAPFGGVK-ASGVGRENSKEAIKHFSQVKSVYVR 477 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: 562 Number of extensions: 28 Number of successful extensions: 6 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: 485 Length adjustment: 34 Effective length of query: 454 Effective length of database: 451 Effective search space: 204754 Effective search space used: 204754 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