GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolE in Rhizobium freirei PRF 81

Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate WP_004124227.1 RHSP_RS23485 myo-inosose-2 dehydratase

Query= reanno::HerbieS:HSERO_RS12135
         (306 letters)



>NCBI__GCF_000359745.1:WP_004124227.1
          Length = 301

 Score =  267 bits (682), Expect = 3e-76
 Identities = 143/296 (48%), Positives = 184/296 (62%), Gaps = 4/296 (1%)

Query: 4   PFNVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRAVLG 63
           P  V++ ++P+SW ND L  LG +  +E  L++ +  GY+G ELG KFPR  E LR +LG
Sbjct: 6   PMGVRLAVSPLSWANDVLEDLGADITVETCLADASGTGYQGIELGRKFPRDAEVLRPLLG 65

Query: 64  KYQLECVSGWYSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGAPT--PL 121
            Y L   SGW+SG+LA RSV+EE+ AV +H  LL A G QVMVYGEVA    G+P   P+
Sbjct: 66  NYGLSLASGWHSGELAERSVDEEMAAVASHARLLRAMGCQVMVYGEVAMMSPGSPLDQPM 125

Query: 122 YQRPRFGSEAAWQGYAQRLDQFARHLL-QRGVRLAYHHHMGAYVETPEDLDKLMALTGEE 180
            QR     E    GYA RL +F+  LL + G++LAYHHH+    ET  ++ +L  L G E
Sbjct: 126 SQRMIMPKEDV-PGYAARLTEFSIRLLGEYGLKLAYHHHLMMVAETYGEISRLFDLAGNE 184

Query: 181 VGLLFDSGHIAFAGGDPLAVLQRHLDRVCHVHCKDVRPAVVKLARNRDWSFLQAVINGAF 240
            GLL D+GH A  G D   ++ R  DR+ H+H KDVR AV+   R RD SF   V  G F
Sbjct: 185 TGLLLDTGHCAGGGFDYRRLIDRFGDRIVHIHLKDVRGAVMDEVRQRDLSFNTGVRRGMF 244

Query: 241 TVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPAVAPSYRYAQMGYRHLSTLVAA 296
           TVPGDG IDF+PL + +   GY GWLVVEAEQDPAVAP+        +H+S +  A
Sbjct: 245 TVPGDGNIDFSPLARFVRDSGYQGWLVVEAEQDPAVAPARAAVTRAVQHVSKVFEA 300


Lambda     K      H
   0.320    0.137    0.417 

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: 291
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: 306
Length of database: 301
Length adjustment: 27
Effective length of query: 279
Effective length of database: 274
Effective search space:    76446
Effective search space used:    76446
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: 48 (23.1 bits)

Align candidate WP_004124227.1 RHSP_RS23485 (myo-inosose-2 dehydratase)
to HMM TIGR04379 (iolE: myo-inosose-2 dehydratase (EC 4.2.1.44))

# 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/TIGR04379.hmm
# target sequence database:        /tmp/gapView.1955908.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04379  [M=290]
Accession:   TIGR04379
Description: myo_inos_iolE: myo-inosose-2 dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      3e-99  318.2   0.0    3.4e-99  318.0   0.0    1.0  1  NCBI__GCF_000359745.1:WP_004124227.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359745.1:WP_004124227.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.0   0.0   3.4e-99   3.4e-99       2     288 ..       9     296 ..       8     298 .. 0.97

  Alignments for each domain:
  == domain 1  score: 318.0 bits;  conditional E-value: 3.4e-99
                             TIGR04379   2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgwfsalll 74 
                                           v+l+++P++W nd l++lg+d+t+e++l++a+  g++g+Elg+kfp+d++vL+++l ++gl+l+sgw s++l+
  NCBI__GCF_000359745.1:WP_004124227.1   9 VRLAVSPLSWANDVLEDLGADITVETCLADASGTGYQGIELGRKFPRDAEVLRPLLGNYGLSLASGWHSGELA 81 
                                           89*********************************************************************** PP

                             TIGR04379  75 eksveeeieavrehlellkalgakvivvaEvgksiqgdk.dtplaerpklteeeweelaeklnklg.eilkek 145
                                           e+sv+ee++av++h++ll+a+g++v+v++Ev+    g++ d+p+++r+ + +e++  +a++l++++ ++l e+
  NCBI__GCF_000359745.1:WP_004124227.1  82 ERSVDEEMAAVASHARLLRAMGCQVMVYGEVAMMSPGSPlDQPMSQRMIMPKEDVPGYAARLTEFSiRLLGEY 154
                                           ********************************98777653899**********************845677** PP

                             TIGR04379 146 glklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadRiahvHlKDvRkevle 218
                                           glklayHhHl  v et  ei rl +l+++e  gll+DtGH + +g d+ +++++++dRi+h+HlKDvR +v++
  NCBI__GCF_000359745.1:WP_004124227.1 155 GLKLAYHHHLMMVAETYGEISRLFDLAGNE-TGLLLDTGHCAGGGFDYRRLIDRFGDRIVHIHLKDVRGAVMD 226
                                           ****************************99.9***************************************** PP

                             TIGR04379 219 evrkekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPakaepleyakkakkylee 288
                                           evr+++ sF ++v++G+ftvPGdG idf+++++ ++ ++Y+GWlvvEaEqDPa+a++ +  + a +++++
  NCBI__GCF_000359745.1:WP_004124227.1 227 EVRQRDLSFNTGVRRGMFTVPGDGNIDFSPLARFVRDSGYQGWLVVEAEQDPAVAPARAAVTRAVQHVSK 296
                                           *********************************************************9999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (290 nodes)
Target sequences:                          1  (301 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 13.23
//
[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