Alignments for a candidate for xacF in Paraburkholderia sp. CCGE1002

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacF in Paraburkholderia sp. CCGE1002

Align Alpha-ketoglutaric semialdehyde dehydrogenase 2; alphaKGSA dehydrogenase 2; 2,5-dioxovalerate dehydrogenase 2; KGSADH-II; EC 1.2.1.26 (characterized)
to candidate WP_013091512.1 BC1002_RS18470 aldehyde dehydrogenase (NADP(+))

Query= SwissProt::Q08IC0
         (525 letters)



>NCBI__GCF_000092885.1:WP_013091512.1
          Length = 527

 Score =  654 bits (1688), Expect = 0.0
 Identities = 334/523 (63%), Positives = 395/523 (75%)

Query: 1   MQLTGEMLIGAEAVAGSAGTLRAFDPSKGEPIDAPVFGVAAQADVERACELARDAFDAYR 60
           M +TG+MLIG +AV G    LRAF+P+ G  I  PVFG     +VE+AC LA+ AFDAYR
Sbjct: 1   MPITGDMLIGRKAVRGEEKPLRAFNPATGSEIAEPVFGSGTVENVEQACALAQQAFDAYR 60

Query: 61  AQPLAARAAFLEAIADEIVALGDALIERAHAETGLPVARLQGERGRTVGQLRLFARVVRD 120
             PLA RA FL+ IAD I ALGD LIERA AE+GLP ARL+GERGRT GQL+LFA+ VR 
Sbjct: 61  QLPLAVRAEFLDRIADGITALGDELIERAMAESGLPKARLEGERGRTTGQLKLFAQTVRA 120

Query: 121 GRFLAASIDPAQPARTPLPRSDLRLQKVGLGPVVVFGASNFPLAFSVAGGDTASALAAGC 180
           G++L A++D   P R PLPRSDLR+QK+ LGPV VFGASNFPLAFSVAGGDTA+ALAAGC
Sbjct: 121 GQWLNATLDSPLPDRKPLPRSDLRMQKIALGPVAVFGASNFPLAFSVAGGDTAAALAAGC 180

Query: 181 PVIVKAHEAHLGTSELVGRAIRAAVAKTGMPAGVFSLLVGPGRVIGGALVSHPAVQAVGF 240
           PV+VKAH AHLGTSELVGR I+    +  +P GVFS++VG G  +G ALV+HPA++AVGF
Sbjct: 181 PVVVKAHRAHLGTSELVGRVIQRVAQEMDLPEGVFSMIVGAGNSVGEALVAHPAIKAVGF 240

Query: 241 TGSRQGGMALVQIANARPQPIPVYAEMSSINPVVLFPAALAARGDAIATGFVDSLTLGVG 300
           TGSR GG +L+++A ARP+PIPVYAEMSSINPV L P AL ARGD+IA GFVDSL LG G
Sbjct: 241 TGSRAGGTSLMRVAAARPEPIPVYAEMSSINPVFLLPNALTARGDSIARGFVDSLVLGAG 300

Query: 301 QFCTNPGLVLAIDGPDLDRFETVAAQALAKKPAGVMLTQGIADAYRNGRGKLAELPGVRE 360
           QFCTNPGL +AID   L  F   A++ALA KPA  MLT GI  AY +G GKLA   GV  
Sbjct: 301 QFCTNPGLAIAIDSDALKGFVATASEALAAKPAQTMLTSGIHAAYEDGEGKLAATKGVEV 360

Query: 361 IGAGEAAQTDCQAGGALYEVGAQAFLAEPAFSHEVFGPASLIVRCRDLDEVARVLEALEG 420
           +  G AA    QA  AL+   AQ FLA  A   EVFGP S I+RC+D  E+ +V E   G
Sbjct: 361 VARGVAATGPTQACAALFVTDAQTFLANAALEDEVFGPVSTIIRCKDEQEMLKVAEHFAG 420

Query: 421 QLTATLQMDADDKPLARRLLPVLERKAGRLLVNGYPTGVEVCDAMVHGGPFPATSNPAVT 480
           QLTATLQMD+ D   A++L+P+LERKAGR+LVNG+PTGVEVC AMVHGGPFPATS+   T
Sbjct: 421 QLTATLQMDSADVAAAKKLVPILERKAGRILVNGFPTGVEVCHAMVHGGPFPATSDSRAT 480

Query: 481 SVGATAIERFLRPVCYQDFPDDLLPEGLQESNPLAIPRLRDGK 523
           SVG T+I+RFLRPVCYQDFP +LLP+ L + NPL + R RDG+
Sbjct: 481 SVGTTSIDRFLRPVCYQDFPAELLPQALADGNPLELWRRRDGE 523


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: 955
Number of extensions: 31
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: 527
Length adjustment: 35
Effective length of query: 490
Effective length of database: 492
Effective search space:   241080
Effective search space used:   241080
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 24 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:

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
the source code
instructions for running GapMind on your computer

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