GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolC in Phaeacidiphilus oryzae TH49

Align 5-dehydro-2-deoxygluconokinase; EC 2.7.1.92; 2-deoxy-5-keto-D-gluconate kinase; DKG kinase (uncharacterized)
to candidate WP_084703970.1 BS73_RS11395 5-dehydro-2-deoxygluconokinase

Query= curated2:Q898F0
         (339 letters)



>NCBI__GCF_000744815.1:WP_084703970.1
          Length = 385

 Score =  166 bits (421), Expect = 7e-46
 Identities = 108/335 (32%), Positives = 165/335 (49%), Gaps = 24/335 (7%)

Query: 11  PLDVIPIGRVTIDFNPNEINRPLEESRTFTKYLGGSPGNIAVGLARLGKKVGFLSTVSDD 70
           P D+I +GR+ +D  P +I  PL E  TF K+LGGS  N+AV  ARL ++   +S    D
Sbjct: 19  PFDLITMGRIGVDIYPLQIGVPLAEVETFGKFLGGSATNVAVAAARLRRRSAVVSRTGAD 78

Query: 71  QFGNFVVNYLKNEGIDISQINRAKNGEKLGLTFTEILSPKESSILMYRKGIA-DLQLSSK 129
            FG +V   L+  G+D   +   +      +TF EI  P +  I  YR+  A DL++  +
Sbjct: 79  PFGEYVHRALREFGVDDRWVTPVQR-YPTPVTFCEIFPPDDFPIWFYRRPKAPDLEIHPE 137

Query: 130 EVSEDYIKSAKAIVISGTALSKSPSREAAFVAL--EYAKKHNTRIIFDLDYREYTWN--- 184
           E+  D I+SA    I+GT L + PSR A   AL    A+      +FDLD+R   W    
Sbjct: 138 ELDLDAIRSAGIFWITGTGLCEEPSRTATLAALAARSARPGAGPTVFDLDWRPAFWGGEG 197

Query: 185 ------------CKEEIAIYYSLAARMSDVIMGSREEFNLMEGLISPEESNDKETAERWI 232
                          E    Y  A   + V +G+ +E  +  GL  P+       AE  +
Sbjct: 198 GASGDGGEGGARAMAEARPIYREALAHATVAVGNLDEAEVATGLRDPQAC-----AEALL 252

Query: 233 GYGNKIVVIKHGKDGSTAYLHDGTSYKIKPFPVKLLKSFGGGDAYASAFIYGIMEGWDVI 292
             G ++ V+K G  G  A   DGT  ++ P PV+++   G GDA+  A  +G++ GW + 
Sbjct: 253 ELGAELAVVKQGPKGVLALHRDGTRAQVPPVPVEVVNGLGAGDAFGGALCHGLLAGWPLE 312

Query: 293 DALEFGSASAAMLVASHSCSEAMPKVEEIKQFIKE 327
             + + +A+ A++    +CS AMP  EEI+Q + E
Sbjct: 313 RTVRWANAAGAIVAGRLACSSAMPTPEEIEQRLTE 347


Lambda     K      H
   0.315    0.134    0.381 

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: 262
Number of extensions: 11
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: 339
Length of database: 385
Length adjustment: 29
Effective length of query: 310
Effective length of database: 356
Effective search space:   110360
Effective search space used:   110360
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 (21.5 bits)
S2: 49 (23.5 bits)

Align candidate WP_084703970.1 BS73_RS11395 (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.2522704.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-113  363.8   0.0   4.5e-113  363.6   0.0    1.0  1  NCBI__GCF_000744815.1:WP_084703970.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000744815.1:WP_084703970.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.6   0.0  4.5e-113  4.5e-113       2     307 ..      20     343 ..      19     345 .. 0.97

  Alignments for each domain:
  == domain 1  score: 363.6 bits;  conditional E-value: 4.5e-113
                             TIGR04382   2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreelereg 74 
                                           +dlit+GR+gvD+y+ qig++l++v++f k+lGGs++N+av+aarl +++a++++ g+d +G++v+++l+++g
  NCBI__GCF_000744815.1:WP_084703970.1  20 FDLITMGRIGVDIYPLQIGVPLAEVETFGKFLGGSATNVAVAAARLRRRSAVVSRTGADPFGEYVHRALREFG 92 
                                           8************************************************************************ PP

                             TIGR04382  75 vdtshvvtdkeartslvlleikdpdefpllfYRe.naaDlaltvddvdeeliaeakallvsgtalskepsrea 146
                                           vd+++v+  + + t+++++ei++pd+fp++fYR+ +a+Dl+++++++d ++i++a +++++gt+l++epsr+a
  NCBI__GCF_000744815.1:WP_084703970.1  93 VDDRWVTPVQRYPTPVTFCEIFPPDDFPIWFYRRpKAPDLEIHPEELDLDAIRSAGIFWITGTGLCEEPSRTA 165
                                           **********************************9************************************** PP

                             TIGR04382 147 vlkale..lakkagvkvvlDiDYRpvlWk...............skeeasaalqlvlkkvdviiGteeEfeia 202
                                           +l+al    a+     +v+D+D+Rp +W+               + +ea+  ++++l++++v++G+ +E e+a
  NCBI__GCF_000744815.1:WP_084703970.1 166 TLAALAarSARPGAGPTVFDLDWRPAFWGgeggasgdggeggarAMAEARPIYREALAHATVAVGNLDEAEVA 238
                                           **99871134445568**************************999999999********************** PP

                             TIGR04382 203 agekddeaaakallelgaelvvvKrGeeGslvytkdeeevevkgfkvevlkvlGaGDaFasgllygllegedl 275
                                            g +d++a a+allelgael+vvK+G++G+l++++d+++ +v++++vev+++lGaGDaF+++l++gll+g++l
  NCBI__GCF_000744815.1:WP_084703970.1 239 TGLRDPQACAEALLELGAELAVVKQGPKGVLALHRDGTRAQVPPVPVEVVNGLGAGDAFGGALCHGLLAGWPL 311
                                           ************************************************************************* PP

                             TIGR04382 276 ekalelanAagaivvsrlscaeamptleelee 307
                                           e+++++anAagaiv+ rl+c+ ampt ee+e+
  NCBI__GCF_000744815.1:WP_084703970.1 312 ERTVRWANAAGAIVAGRLACSSAMPTPEEIEQ 343
                                           ******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (385 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: 19.28
//
[ok]

This GapMind analysis is from Apr 09 2024. 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