Alignments for a candidate for xad in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments for a candidate for xad in Caulobacter crescentus NA1000

Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate CCNA_01488 CCNA_01488 dihydroxyacid dehydratase

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



>FitnessBrowser__Caulo:CCNA_01488
          Length = 600

 Score =  752 bits (1942), Expect = 0.0
 Identities = 367/596 (61%), Positives = 456/596 (76%), Gaps = 4/596 (0%)

Query: 3   DTPKHRLRSEQWFNDPAHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNR 62
           + P+  LRS  WF++P + DMTALY+ERY+N+G+T EELQSG+PIIGIAQTGSDL+PCNR
Sbjct: 5   NVPRRALRSRAWFDNPDNIDMTALYLERYLNFGLTLEELQSGKPIIGIAQTGSDLSPCNR 64

Query: 63  HHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGV 122
           HHL LA+RV+ GIR AGGI +EFPVHPI E  +RPTA LDRNL+YLGLVE+L+GYPLDGV
Sbjct: 65  HHLVLAERVREGIRSAGGIALEFPVHPIQETGKRPTAGLDRNLSYLGLVELLYGYPLDGV 124

Query: 123 VLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEI 182
           VLT GCDKTTPACLMAAAT ++PAI LS GPML+G HKG+  GSGT++W AR ++AAGEI
Sbjct: 125 VLTIGCDKTTPACLMAAATVNIPAIALSVGPMLNGWHKGKRTGSGTIVWKAREMLAAGEI 184

Query: 183 DYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATG 242
           D  GF+++  +++PS G+CNTMGTA +MN+L EALGMSLPG A+IPAPYR+R + AY TG
Sbjct: 185 DNAGFIKLVASSAPSTGYCNTMGTATTMNSLTEALGMSLPGSAAIPAPYRDRQENAYRTG 244

Query: 243 KRICDLVRQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQR 302
            RI ++V +D++PS I+TR+AF NAI V SA+G S+N P HL A+ARHM V+L+LEDW+ 
Sbjct: 245 LRIVEMVAEDLKPSDILTREAFLNAIVVNSAIGGSTNAPIHLNALARHMDVDLTLEDWET 304

Query: 303 IGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSNS 362
            G+DVPLLVN  PAG+YLGE ++RAGGVP+V  +L + G +H+D   VSG++IGE    +
Sbjct: 305 AGKDVPLLVNLQPAGEYLGEDYYRAGGVPAVFGQLIEQGLIHQDARAVSGQSIGEQYRGA 364

Query: 363 LTSNTDVIHPFDTPLKHRAGFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFEAR 422
           +  + DVI PF  PL   AGF ++ GN F+SAIMK SV+ E FR  YLS P   ++FE  
Sbjct: 365 VIEDEDVIRPFARPLVEHAGFAIMRGNLFNSAIMKTSVISEEFRARYLSNPDDPDAFEGN 424

Query: 423 AIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDSL 482
           AIVF+GPEDYH RIDDPAL I    IL +RG G +GYPGSAEVVNM  P  LIKQGI  L
Sbjct: 425 AIVFDGPEDYHHRIDDPALGITAYSILFMRGAGPIGYPGSAEVVNMRAPNYLIKQGIHQL 484

Query: 483 PCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRLKVDLNTRTVNLLIDDAEMAQR 542
           PC+GDGRQSGTS SPSILN SPEAA GGGLALLKT DR++ DL    V++L+  +E+ +R
Sbjct: 485 PCIGDGRQSGTSGSPSILNASPEAAAGGGLALLKTGDRVRFDLRKSRVDVLVSASEVVER 544

Query: 543 RREWIP----NIPPSQTPWQELYRQLVGQLSTGGCLEPATLHLRVIARSGEPRHSH 594
           RR          P SQTPWQE+ R +VGQ+ TG  LEPA  + R+    G PR +H
Sbjct: 545 RRALEAAGGYAYPESQTPWQEIQRAVVGQMDTGAVLEPAVKYQRIAQTKGLPRDNH 600


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: 1124
Number of extensions: 52
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: 600
Length adjustment: 37
Effective length of query: 557
Effective length of database: 563
Effective search space:   313591
Effective search space used:   313591
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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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