GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolC in Rhodococcus qingshengii djl-6-2

Align 5-dehydro-2-deoxygluconokinase; EC 2.7.1.92; 2-deoxy-5-keto-D-gluconate kinase; DKG kinase (uncharacterized)
to candidate WP_050654911.1 C1M55_RS10205 5-dehydro-2-deoxygluconokinase

Query= curated2:Q6LK43
         (331 letters)



>NCBI__GCF_002893965.1:WP_050654911.1
          Length = 322

 Score =  172 bits (437), Expect = 8e-48
 Identities = 115/323 (35%), Positives = 164/323 (50%), Gaps = 18/323 (5%)

Query: 9   DRPLDAIVLGRAGVDLYAREANTDMADISGFNKFVGGSAANIAVAISKLGGKVGFIGCVA 68
           D P D + +GR+GVD+Y  +    + D+  F KF+GGSAAN++VA ++LG +   I  V 
Sbjct: 3   DAPFDVLAIGRSGVDIYPLQTGVGLEDVETFGKFLGGSAANVSVAAARLGRRAALISGVG 62

Query: 69  DDAFGGYVRGYMTEQGINLDGMMTDNSGSRTSVAFTEM-KPNDCTVLIYRN-KASDLTLK 126
            D FG +V   +   G++ +  +  NS   T V F E+  P+D  +  YR   A DL + 
Sbjct: 63  SDPFGKFVTRELARLGVD-NRFVVTNSEYPTPVTFCEIFPPDDFPLYFYRKPHAPDLRIT 121

Query: 127 PEQVDPAYIAQSKMLVVTGTALSESPSREATLIAMEHARRSNTVVVLDVDYRPYSWRTDV 186
           PE +D   +  + +   T T LSE PSR A   A E AR    + VLD+DYRP  W T  
Sbjct: 122 PEDIDLDAVRTASLYWSTVTGLSEEPSRSAHFAAWE-ARERRPLTVLDLDYRPMFWSTPQ 180

Query: 187 DASIYYGIAAGLSDIVIGNREEFDMMETVLAPGNTDDDATADRFLRANTQVVIVKAGELG 246
           +A+     A     + +GNREE +     +A G T+ +  AD  L    ++ IVK G  G
Sbjct: 181 EATTQVQRALAHVTVAVGNREECE-----IAVGETNPNKAADALLDLGVELAIVKQGPKG 235

Query: 247 SKVYCKDGHKFQQGIF----RVEVKKPFGSGDSFAGGLIWTLVNGGELEDGVKHGSAAAA 302
                  G   +Q I      V+V    G+GDSF G L   L+ G  LE  +++ +AA A
Sbjct: 236 VL-----GKTRKQSITVPPNAVDVVNGLGAGDSFGGSLCHGLLAGWPLEKVLRYANAAGA 290

Query: 303 INVSGNSCTEAMPTKEVLFDFIE 325
           I  S   C+ AMPT E + D  E
Sbjct: 291 IVASRLECSTAMPTAEEVHDLAE 313


Lambda     K      H
   0.317    0.134    0.384 

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: 258
Number of extensions: 13
Number of successful extensions: 5
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: 331
Length of database: 322
Length adjustment: 28
Effective length of query: 303
Effective length of database: 294
Effective search space:    89082
Effective search space used:    89082
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_050654911.1 C1M55_RS10205 (5-dehydro-2-deoxygluconokinase)
to HMM TIGR04382 (iolC: 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR04382.hmm
# target sequence database:        /tmp/gapView.2754054.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04382  [M=309]
Accession:   TIGR04382
Description: myo_inos_iolC_N: 5-dehydro-2-deoxygluconokinase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-122  394.1   0.0   2.5e-122  393.9   0.0    1.0  1  NCBI__GCF_002893965.1:WP_050654911.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050654911.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.9   0.0  2.5e-122  2.5e-122       2     307 ..       6     310 ..       5     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 393.9 bits;  conditional E-value: 2.5e-122
                             TIGR04382   2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreelereg 74 
                                           +d+++iGR+gvD+y+ q+g+ ledv++f k+lGGs+aN++v+aarlG+++ali+ vg d +G+fv++el+r g
  NCBI__GCF_002893965.1:WP_050654911.1   6 FDVLAIGRSGVDIYPLQTGVGLEDVETFGKFLGGSAANVSVAAARLGRRAALISGVGSDPFGKFVTRELARLG 78 
                                           8************************************************************************ PP

                             TIGR04382  75 vdtshvvtdkeartslvlleikdpdefpllfYRe.naaDlaltvddvdeeliaeakallvsgtalskepsrea 146
                                           vd ++vvt++e+ t+++++ei++pd+fpl+fYR+ +a+Dl +t++d+d ++++ a++ + ++t+ls+epsr+a
  NCBI__GCF_002893965.1:WP_050654911.1  79 VDNRFVVTNSEYPTPVTFCEIFPPDDFPLYFYRKpHAPDLRITPEDIDLDAVRTASLYWSTVTGLSEEPSRSA 151
                                           **********************************9************************************** PP

                             TIGR04382 147 vlkalelakkagvkvvlDiDYRpvlWkskeeasaalqlvlkkvdviiGteeEfeiaagekddeaaakallelg 219
                                           +++a+e a++++  +vlD+DYRp++W++++ea++++q++l++v+v++G++eE+eia+ge+++++aa+all+lg
  NCBI__GCF_002893965.1:WP_050654911.1 152 HFAAWE-ARERRPLTVLDLDYRPMFWSTPQEATTQVQRALAHVTVAVGNREECEIAVGETNPNKAADALLDLG 223
                                           ******.****************************************************************** PP

                             TIGR04382 220 aelvvvKrGeeGslvytkdeeevevkgfkvevlkvlGaGDaFasgllygllegedlekalelanAagaivvsr 292
                                           +el++vK+G++G+l  t++ ++++v++  v+v+++lGaGD+F+++l++gll+g++lek+l++anAagaiv+sr
  NCBI__GCF_002893965.1:WP_050654911.1 224 VELAIVKQGPKGVLGKTRK-QSITVPPNAVDVVNGLGAGDSFGGSLCHGLLAGWPLEKVLRYANAAGAIVASR 295
                                           ******************9.***************************************************** PP

                             TIGR04382 293 lscaeamptleelee 307
                                           l+c++ampt+ee+++
  NCBI__GCF_002893965.1:WP_050654911.1 296 LECSTAMPTAEEVHD 310
                                           ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (322 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.01
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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