Alignments for a candidate for araB in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for araB in Escherichia coli BW25113

Align ribulokinase; EC 2.7.1.16 (characterized)
to candidate 14209 b0063 ribulokinase (NCBI)

Query= CharProtDB::CH_002149
         (566 letters)



>FitnessBrowser__Keio:14209
          Length = 566

 Score = 1154 bits (2986), Expect = 0.0
 Identities = 566/566 (100%), Positives = 566/566 (100%)

Query: 1   MAIAIGLDFGSDSVRALAVDCATGEEIATSVEWYPRWQKGQFCDAPNNQFRHHPRDYIES 60
           MAIAIGLDFGSDSVRALAVDCATGEEIATSVEWYPRWQKGQFCDAPNNQFRHHPRDYIES
Sbjct: 1   MAIAIGLDFGSDSVRALAVDCATGEEIATSVEWYPRWQKGQFCDAPNNQFRHHPRDYIES 60

Query: 61  MEAALKTVLAELSVEQRAAVVGIGVDSTGSTPAPIDADGNVLALRPEFAENPNAMFVLWK 120
           MEAALKTVLAELSVEQRAAVVGIGVDSTGSTPAPIDADGNVLALRPEFAENPNAMFVLWK
Sbjct: 61  MEAALKTVLAELSVEQRAAVVGIGVDSTGSTPAPIDADGNVLALRPEFAENPNAMFVLWK 120

Query: 121 DHTAVEEAEEITRLCHAPGNVDYSRYIGGIYSSEWFWAKILHVTRQDSAVAQSAASWIEL 180
           DHTAVEEAEEITRLCHAPGNVDYSRYIGGIYSSEWFWAKILHVTRQDSAVAQSAASWIEL
Sbjct: 121 DHTAVEEAEEITRLCHAPGNVDYSRYIGGIYSSEWFWAKILHVTRQDSAVAQSAASWIEL 180

Query: 181 CDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPASFFDELDPILNRHLPSPLFT 240
           CDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPASFFDELDPILNRHLPSPLFT
Sbjct: 181 CDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPASFFDELDPILNRHLPSPLFT 240

Query: 241 DTWTADIPVGTLCPEWAQRLGLPESVVISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDI 300
           DTWTADIPVGTLCPEWAQRLGLPESVVISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDI
Sbjct: 241 DTWTADIPVGTLCPEWAQRLGLPESVVISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDI 300

Query: 301 LIADKQSVGERAVKGICGQVDGSVVPGFIGLEAGQSAFGDIYAWFGRVLGWPLEQLAAQH 360
           LIADKQSVGERAVKGICGQVDGSVVPGFIGLEAGQSAFGDIYAWFGRVLGWPLEQLAAQH
Sbjct: 301 LIADKQSVGERAVKGICGQVDGSVVPGFIGLEAGQSAFGDIYAWFGRVLGWPLEQLAAQH 360

Query: 361 PELKTQINASQKQLLPALTEAWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLA 420
           PELKTQINASQKQLLPALTEAWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLA
Sbjct: 361 PELKTQINASQKQLLPALTEAWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLA 420

Query: 421 TDAPLLFGGLIAATAFGARAIMECFTDQGIAVNNVMALGGIARKNQVIMQACCDVLNRPL 480
           TDAPLLFGGLIAATAFGARAIMECFTDQGIAVNNVMALGGIARKNQVIMQACCDVLNRPL
Sbjct: 421 TDAPLLFGGLIAATAFGARAIMECFTDQGIAVNNVMALGGIARKNQVIMQACCDVLNRPL 480

Query: 481 QIVASDQCCALGAAIFAAVAAKVHADIPSAQQKMASAVEKTLQPCSEQAQRFEQLYRRYQ 540
           QIVASDQCCALGAAIFAAVAAKVHADIPSAQQKMASAVEKTLQPCSEQAQRFEQLYRRYQ
Sbjct: 481 QIVASDQCCALGAAIFAAVAAKVHADIPSAQQKMASAVEKTLQPCSEQAQRFEQLYRRYQ 540

Query: 541 QWAMSAEQHYLPTSAPAQAAQAVATL 566
           QWAMSAEQHYLPTSAPAQAAQAVATL
Sbjct: 541 QWAMSAEQHYLPTSAPAQAAQAVATL 566


Lambda     K      H
   0.320    0.133    0.419 

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: 1269
Number of extensions: 37
Number of successful extensions: 1
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: 566
Length of database: 566
Length adjustment: 36
Effective length of query: 530
Effective length of database: 530
Effective search space:   280900
Effective search space used:   280900
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: 53 (25.0 bits)

Align candidate 14209 b0063 (ribulokinase (NCBI))
to HMM TIGR01234 (araB: ribulokinase (EC 2.7.1.16))

# 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/TIGR01234.hmm
# target sequence database:        /tmp/gapView.32722.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01234  [M=536]
Accession:   TIGR01234
Description: L-ribulokinase: ribulokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.8e-288  943.5   0.2   2.1e-288  943.4   0.2    1.0  1  lcl|FitnessBrowser__Keio:14209  b0063 ribulokinase (NCBI)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:14209  b0063 ribulokinase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  943.4   0.2  2.1e-288  2.1e-288       1     535 [.       2     552 ..       2     553 .. 0.99

  Alignments for each domain:
  == domain 1  score: 943.4 bits;  conditional E-value: 2.1e-288
                       TIGR01234   1 ayaiGvdfGtlsgralvvdvatGeelaaavkeyrravvdevldkteaklPadyalqhPadyievleaaikevlaelgvd 79 
                                     a+aiG+dfG++s+ral+vd+atGee+a++v++y+r+++++++d   a  P++++++hP+dyie++eaa+k+vlael+v+
  lcl|FitnessBrowser__Keio:14209   2 AIAIGLDFGSDSVRALAVDCATGEEIATSVEWYPRWQKGQFCD---A--PNNQFRHHPRDYIESMEAALKTVLAELSVE 75 
                                     699****************************************...6..****************************** PP

                       TIGR01234  80 p.advvGiGvdftastivpidsdGnvlallpefaeePhayvklWkdhaaqeeadrinrlaeaeGevflsryg.Glisse 156
                                     + a+vvGiGvd+t+st++pid+dGnvlal+pefae+P+a+++lWkdh+a+eea++i+rl++a+G+v++sry+ G++sse
  lcl|FitnessBrowser__Keio:14209  76 QrAAVVGIGVDSTGSTPAPIDADGNVLALRPEFAENPNAMFVLWKDHTAVEEAEEITRLCHAPGNVDYSRYIgGIYSSE 154
                                     *9*********************************************************************999***** PP

                       TIGR01234 157 WlfakvlqiaeedpeiyeaadrwieaadWivaqlsG.....dlkrsrctaGykalwseskg.yPsasfleelnPslkri 229
                                     W++ak+l+++++d++++++a++wie++dW++a+lsG     d++r+rc+aG+k+lw+es+g +P+asf++el+P+l+r+
  lcl|FitnessBrowser__Keio:14209 155 WFWAKILHVTRQDSAVAQSAASWIELCDWVPALLSGttrpqDIRRGRCSAGHKSLWHESWGgLPPASFFDELDPILNRH 233
                                     ************************************************************99***************** PP

                       TIGR01234 230 vkdkletdigsvgekaGtltekaakllGlpegvvvavgnvdahvsaaaagiaePgklvkiiGtstcdvllgekl....r 304
                                     ++++l+td++++++++Gtl++++a++lGlpe+vv+++g++d+h++a++ag a+P++lvk+iGtstcd+l+++k+    r
  lcl|FitnessBrowser__Keio:14209 234 LPSPLFTDTWTADIPVGTLCPEWAQRLGLPESVVISGGAFDCHMGAVGAG-AQPNALVKVIGTSTCDILIADKQsvgeR 311
                                     **************************************************.***********************9**** PP

                       TIGR01234 305 avkGicGvvdggivpGfiGyeaGqsavGdifaWfvkvl.........vppelkeeakekqlqllealsekaakqesgeh 374
                                     avkGicG+vdg++vpGfiG+eaGqsa+Gdi+aWf++vl         ++pelk++++++q+qll+al+e++ak++s++h
  lcl|FitnessBrowser__Keio:14209 312 AVKGICGQVDGSVVPGFIGLEAGQSAFGDIYAWFGRVLgwpleqlaaQHPELKTQINASQKQLLPALTEAWAKNPSLDH 390
                                     ******************************************************************************* PP

                       TIGR01234 375 glvaldWfnGnrsvlvdarlkGvlvgltlatkaeelyralveatafGtrmivetfkesGvaveellaaGGiaeknplvm 453
                                     ++v+ldWfnG+r++++++rlkGv+++l+lat+a+ l+++l++atafG+r+i+e+f+++G+av++++a+GGia+kn+++m
  lcl|FitnessBrowser__Keio:14209 391 LPVVLDWFNGRRTPNANQRLKGVITDLNLATDAPLLFGGLIAATAFGARAIMECFTDQGIAVNNVMALGGIARKNQVIM 469
                                     ******************************************************************************* PP

                       TIGR01234 454 qiyadvlnlplkivasdqapalGaaifaavaageyadipkaaakmgsavektltPisenaaryeklyaeykeladyfgk 532
                                     q+++dvln+pl+ivasdq++alGaaifaavaa+++adip+a++km+savektl+P+se+a+r+e+ly++y+++a+++++
  lcl|FitnessBrowser__Keio:14209 470 QACCDVLNRPLQIVASDQCCALGAAIFAAVAAKVHADIPSAQQKMASAVEKTLQPCSEQAQRFEQLYRRYQQWAMSAEQ 548
                                     ******************************************************************************9 PP

                       TIGR01234 533 .enp 535
                                      ++p
  lcl|FitnessBrowser__Keio:14209 549 hYLP 552
                                     6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (536 nodes)
Target sequences:                          1  (566 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 9.80
//
[ok]

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

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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