Alignments for a candidate for xad in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Cupriavidus basilensis 4G11

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate RR42_RS33950 RR42_RS33950 dihydroxy-acid dehydratase

Query= reanno::pseudo6_N2E2:Pf6N2E2_1668
         (594 letters)



>FitnessBrowser__Cup4G11:RR42_RS33950
          Length = 577

 Score =  441 bits (1135), Expect = e-128
 Identities = 255/592 (43%), Positives = 347/592 (58%), Gaps = 22/592 (3%)

Query: 6   KHRLRSEQWFNDPAHADMTALYVERYM-NYGMTREELQSGRPIIGIAQTGSDLTPCNRHH 64
           K +LRS QWF     AD        +M N G+   E   GRPIIGI  T S+LTPCN H 
Sbjct: 5   KSKLRSAQWFGS---ADKNGFMYRSWMKNQGIPDHEFD-GRPIIGICNTWSELTPCNAHF 60

Query: 65  LELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVVL 124
            +LA+ VK G+ +AGG P+EFPV    E + RPTA L RNLA + + E + G P+D VVL
Sbjct: 61  RKLAEHVKRGVYEAGGFPVEFPVFSNGESNLRPTAMLTRNLAAMDVEEAIRGNPIDAVVL 120

Query: 125 TTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDY 184
            TGCDKTTPA LM AA+ D+PAIV++GGPML+G   G+ IGSGT +W     + AGEI+ 
Sbjct: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKLDGKNIGSGTAVWQLHESLKAGEINV 180

Query: 185 EGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKR 244
             F+      S S G CNTMGTA +M  +AEALG SLP  A+IPA    R  +A+ +G R
Sbjct: 181 HQFLSAEAGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDSRRYVLAHMSGIR 240

Query: 245 ICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIG 304
           I ++ ++ +  S+I+TR AFENAI   +A+G S+N   HL AIA  +GV L LEDW RIG
Sbjct: 241 IVEMAKEGLTLSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWTRIG 300

Query: 305 EDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRL-HEDCATVSGKTIGEIVSNSL 363
            D P +V+ MP+G++L E F+ AGG+P+V+  L +A  L H D  TV+G+T+ + V ++ 
Sbjct: 301 RDTPTIVDLMPSGRFLMEEFYYAGGLPAVLRRLGEANLLPHPDALTVNGRTLWQNVKDAP 360

Query: 364 TSNTDVIHPFDTPLKHRAGFIVLSGNFFD-SAIMKMSVVGEAFRKTYLSEPGAENSFEAR 422
            +N +VI   D PL    G  VL GN     A++K S       K              R
Sbjct: 361 NTNDEVIRALDNPLMADGGIRVLRGNLAPRGAVLKPSAATPGLLK-----------HRGR 409

Query: 423 AIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDSL 482
           A+VFE  E Y  RI D  LD+D   ++V++  G  GYPG AEV NM  P  L++QG+  +
Sbjct: 410 AVVFENLEHYKERIVDETLDVDASSVMVLKNCGPKGYPGMAEVGNMGLPPKLLRQGVKDM 469

Query: 483 PCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMAQR 542
             + D R SGT+    +L+++PEAA GG LA ++  D +++D    T++L IDD E+A+R
Sbjct: 470 VRISDARMSGTAYGTVVLHVAPEAAAGGPLAAVRDGDWIELDCEAGTLHLDIDDEELARR 529

Query: 543 RREWIPNIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGEPRHSH 594
             E +      +  ++ LY   V Q   G  L+     L     +  PRHSH
Sbjct: 530 MAERVDTRAAGEGGYRRLYVDHVLQADEGCDLD----FLVGCRGAAVPRHSH 577


Lambda     K      H
   0.319    0.135    0.407 

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: 982
Number of extensions: 65
Number of successful extensions: 3
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: 594
Length of database: 577
Length adjustment: 37
Effective length of query: 557
Effective length of database: 540
Effective search space:   300780
Effective search space used:   300780
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
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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
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