Alignments for a candidate for dopDH in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for dopDH in Paraburkholderia bryophila 376MFSha3.1

Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate H281DRAFT_05316 H281DRAFT_05316 NADP-dependent aldehyde dehydrogenase

Query= SwissProt::Q08IC0
         (525 letters)



>FitnessBrowser__Burk376:H281DRAFT_05316
          Length = 535

 Score =  655 bits (1690), Expect = 0.0
 Identities = 333/522 (63%), Positives = 393/522 (75%)

Query: 2   QLTGEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYRA 61
           ++TGEMLIG ++V G+   L AF+P+ G  I  PVFG     DV  ACELA+ AFD YR 
Sbjct: 10  RITGEMLIGRQSVRGAEEALHAFNPATGADIAEPVFGSGTARDVGLACELAQKAFDPYRQ 69

Query: 62  QPLAARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRDG 121
            PL+ RA FLE IAD I ALGDAL+ERA  E+GLP ARL+GERGRT GQL+LFA+ VR G
Sbjct: 70  LPLSVRAEFLERIADGITALGDALVERAQQESGLPKARLEGERGRTTGQLKLFAQFVRSG 129

Query: 122 RFLAASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGCP 181
           ++L A++D   P R PLPRSDLR+QK+ +GPV VFGASNFPLAFSVAGGDTA+ALAAGCP
Sbjct: 130 QWLDATLDSPLPERKPLPRSDLRMQKIAIGPVAVFGASNFPLAFSVAGGDTAAALAAGCP 189

Query: 182 VIVKAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGFT 241
           V+VKAH AHLGTSE+VGR I+    +  +P GVFSL+VG G  +G ALV+HPA++AVGFT
Sbjct: 190 VVVKAHRAHLGTSEMVGRVIQRVAQEMDLPEGVFSLIVGAGNSVGEALVAHPAIKAVGFT 249

Query: 242 GSRQGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVGQ 301
           GSR GG+AL+++A ARP+PIPV+AEMSSINPV L P AL  R + IA GFVDSL LG GQ
Sbjct: 250 GSRAGGLALMRVAAARPEPIPVFAEMSSINPVFLLPNALTQRTENIARGFVDSLVLGAGQ 309

Query: 302 FCTNPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVREI 361
           FCTNPGL +A+D   L  F  VA++AL  KPA  MLT GI  AY  G  KLA +PGV  +
Sbjct: 310 FCTNPGLAIAVDSDALKNFVAVASEALGGKPAQTMLTSGIHSAYTQGESKLAGIPGVETV 369

Query: 362 GAGEAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEGQ 421
             G       QA  AL+   A+ FLA PA   EVFGPAS IVRC+D +E+ +V E   GQ
Sbjct: 370 ARGVDVTGPNQARAALFVTDAKTFLATPALEDEVFGPASTIVRCKDENELLQVAEHFAGQ 429

Query: 422 LTATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVTS 481
           LTAT+QMD+ D P ARRL+P+LERKAGRLLVNGYPTGVEVC AMVHGGPFPATS+   TS
Sbjct: 430 LTATIQMDSADVPAARRLVPILERKAGRLLVNGYPTGVEVCHAMVHGGPFPATSDSRATS 489

Query: 482 VGATAIERFLRPVCYQDFPDDLLPEGLQESNPLAIPRLRDGK 523
           VG TAIERFLRPVCYQDFP DLLP+ L + NPL + R RDG+
Sbjct: 490 VGTTAIERFLRPVCYQDFPADLLPQALADDNPLDLWRRRDGE 531


Lambda     K      H
   0.320    0.137    0.396 

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: 935
Number of extensions: 29
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: 525
Length of database: 535
Length adjustment: 35
Effective length of query: 490
Effective length of database: 500
Effective search space:   245000
Effective search space used:   245000
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
Organisms (tab-delimited)
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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources