GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF 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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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:

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:

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