GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araB in Klebsiella michiganensis M5al

Align ribulokinase; EC 2.7.1.16 (characterized)
to candidate BWI76_RS04590 BWI76_RS04590 ribulokinase

Query= CharProtDB::CH_002149
         (566 letters)



>FitnessBrowser__Koxy:BWI76_RS04590
          Length = 569

 Score = 1024 bits (2648), Expect = 0.0
 Identities = 495/560 (88%), Positives = 523/560 (93%)

Query: 1   MAIAIGLDFGSDSVRALAVDCATGEEIATSVEWYPRWQKGQFCDAPNNQFRHHPRDYIES 60
           MAIAIGLDFGSDSVRALAV+CATGEE+A SVEWYPRWQ+G FCD PNNQFRHHPRDYIES
Sbjct: 1   MAIAIGLDFGSDSVRALAVECATGEELAASVEWYPRWQEGLFCDGPNNQFRHHPRDYIES 60

Query: 61  MEAALKTVLAELSVEQRAAVVGIGVDSTGSTPAPIDADGNVLALRPEFAENPNAMFVLWK 120
           MEAALK+VLA LS EQRAAVVGIGVDSTGSTPAPIDADGNVLALR EFA NPNAMFVLWK
Sbjct: 61  MEAALKSVLASLSAEQRAAVVGIGVDSTGSTPAPIDADGNVLALRDEFASNPNAMFVLWK 120

Query: 121 DHTAVEEAEEITRLCHAPGNVDYSRYIGGIYSSEWFWAKILHVTRQDSAVAQSAASWIEL 180
           DHT+VEEAEEITRLCH PG  DYSRYIGGIYSSEWFWAKILHVTRQDSAVA++AASWIEL
Sbjct: 121 DHTSVEEAEEITRLCHQPGKEDYSRYIGGIYSSEWFWAKILHVTRQDSAVAEAAASWIEL 180

Query: 181 CDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPASFFDELDPILNRHLPSPLFT 240
           CDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPA FFDELDPI+N++L  P+F+
Sbjct: 181 CDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPAGFFDELDPIINQNLAYPMFS 240

Query: 241 DTWTADIPVGTLCPEWAQRLGLPESVVISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDI 300
           +TWTAD+PVGTL  EWA RLGLP++V ISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDI
Sbjct: 241 ETWTADVPVGTLTAEWAARLGLPQTVAISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDI 300

Query: 301 LIADKQSVGERAVKGICGQVDGSVVPGFIGLEAGQSAFGDIYAWFGRVLGWPLEQLAAQH 360
           LIADKQSVGER VKGICGQVDGSVVP FIG+EAGQSAFGDIYAWFGR+LGWPLEQLA  H
Sbjct: 301 LIADKQSVGERTVKGICGQVDGSVVPDFIGMEAGQSAFGDIYAWFGRILGWPLEQLAQAH 360

Query: 361 PELKTQINASQKQLLPALTEAWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLA 420
           PELK QI ASQKQLLPALT+AWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLA
Sbjct: 361 PELKEQIKASQKQLLPALTDAWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLA 420

Query: 421 TDAPLLFGGLIAATAFGARAIMECFTDQGIAVNNVMALGGIARKNQVIMQACCDVLNRPL 480
           TDAP LFGGLIAATAFGARAIMECFTDQGI VNNVMALGGIARKN VIMQACCDVLNRPL
Sbjct: 421 TDAPALFGGLIAATAFGARAIMECFTDQGIPVNNVMALGGIARKNPVIMQACCDVLNRPL 480

Query: 481 QIVASDQCCALGAAIFAAVAAKVHADIPSAQQKMASAVEKTLQPCSEQAQRFEQLYRRYQ 540
           QIVASDQCCALGAAIFAAVAA V+ DIP+AQ+ MAS VE TLQP   QAQRFEQLY+RYQ
Sbjct: 481 QIVASDQCCALGAAIFAAVAAGVYRDIPAAQENMASQVESTLQPRPAQAQRFEQLYQRYQ 540

Query: 541 QWAMSAEQHYLPTSAPAQAA 560
           QW++SAEQ YLP++A A+ A
Sbjct: 541 QWSLSAEQRYLPSTAKAETA 560


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: 1185
Number of extensions: 39
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: 569
Length adjustment: 36
Effective length of query: 530
Effective length of database: 533
Effective search space:   282490
Effective search space used:   282490
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 BWI76_RS04590 BWI76_RS04590 (ribulokinase)
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.30811.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
     2e-268  877.5   0.1   2.2e-268  877.3   0.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS04590  BWI76_RS04590 ribulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS04590  BWI76_RS04590 ribulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  877.3   0.1  2.2e-268  2.2e-268       1     534 [.       2     551 ..       2     553 .. 0.99

  Alignments for each domain:
  == domain 1  score: 877.3 bits;  conditional E-value: 2.2e-268
                               TIGR01234   1 ayaiGvdfGtlsgralvvdvatGeelaaavkeyrravvdevldkteaklPadyalqhPadyievleaaike 71 
                                             a+aiG+dfG++s+ral+v++atGeelaa+v++y+r++ + ++d      P++++++hP+dyie++eaa+k+
  lcl|FitnessBrowser__Koxy:BWI76_RS04590   2 AIAIGLDFGSDSVRALAVECATGEELAASVEWYPRWQEGLFCD---G--PNNQFRHHPRDYIESMEAALKS 67 
                                             699****************************************...4..9********************* PP

                               TIGR01234  72 vlaelgvdp.advvGiGvdftastivpidsdGnvlallpefaeePhayvklWkdhaaqeeadrinrlaeae 141
                                             vla l+ ++ a+vvGiGvd+t+st++pid+dGnvlal++efa +P+a+++lWkdh+++eea++i+rl++++
  lcl|FitnessBrowser__Koxy:BWI76_RS04590  68 VLASLSAEQrAAVVGIGVDSTGSTPAPIDADGNVLALRDEFASNPNAMFVLWKDHTSVEEAEEITRLCHQP 138
                                             *********9************************************************************* PP

                               TIGR01234 142 Gevflsryg.GlisseWlfakvlqiaeedpeiyeaadrwieaadWivaqlsG.....dlkrsrctaGykal 206
                                             G+ ++sry+ G++sseW++ak+l+++++d++++eaa++wie++dW++a+lsG     d++r+rc+aG+k+l
  lcl|FitnessBrowser__Koxy:BWI76_RS04590 139 GKEDYSRYIgGIYSSEWFWAKILHVTRQDSAVAEAAASWIELCDWVPALLSGttrpqDIRRGRCSAGHKSL 209
                                             ********999************************************************************ PP

                               TIGR01234 207 wseskg.yPsasfleelnPslkrivkdkletdigsvgekaGtltekaakllGlpegvvvavgnvdahvsaa 276
                                             w+es+g +P+a f++el+P++++ +  +++++++++++++Gtlt+++a++lGlp++v++++g++d+h++a+
  lcl|FitnessBrowser__Koxy:BWI76_RS04590 210 WHESWGgLPPAGFFDELDPIINQNLAYPMFSETWTADVPVGTLTAEWAARLGLPQTVAISGGAFDCHMGAV 280
                                             *****99**************************************************************** PP

                               TIGR01234 277 aagiaePgklvkiiGtstcdvllgekl....ravkGicGvvdggivpGfiGyeaGqsavGdifaWfvkvl. 342
                                             +ag a+P++lvk+iGtstcd+l+++k+    r+vkGicG+vdg++vp fiG+eaGqsa+Gdi+aWf++ l 
  lcl|FitnessBrowser__Koxy:BWI76_RS04590 281 GAG-AQPNALVKVIGTSTCDILIADKQsvgeRTVKGICGQVDGSVVPDFIGMEAGQSAFGDIYAWFGRILg 350
                                             ***.***********************9******************************************* PP

                               TIGR01234 343 ........vppelkeeakekqlqllealsekaakqesgehglvaldWfnGnrsvlvdarlkGvlvgltlat 405
                                                      +pelke++k++q+qll+al++++ak++s++h++v+ldWfnG+r++++++rlkGv+++l+lat
  lcl|FitnessBrowser__Koxy:BWI76_RS04590 351 wpleqlaqAHPELKEQIKASQKQLLPALTDAWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLAT 421
                                             *******99************************************************************** PP

                               TIGR01234 406 kaeelyralveatafGtrmivetfkesGvaveellaaGGiaeknplvmqiyadvlnlplkivasdqapalG 476
                                             +a+ l+++l++atafG+r+i+e+f+++G++v++++a+GGia+knp++mq+++dvln+pl+ivasdq++alG
  lcl|FitnessBrowser__Koxy:BWI76_RS04590 422 DAPALFGGLIAATAFGARAIMECFTDQGIPVNNVMALGGIARKNPVIMQACCDVLNRPLQIVASDQCCALG 492
                                             *********************************************************************** PP

                               TIGR01234 477 aaifaavaageyadipkaaakmgsavektltPisenaaryeklyaeykeladyfgk.en 534
                                             aaifaavaag+y+dip a+++m+s+ve tl+P + +a+r+e+ly++y+++  ++++ ++
  lcl|FitnessBrowser__Koxy:BWI76_RS04590 493 AAIFAAVAAGVYRDIPAAQENMASQVESTLQPRPAQAQRFEQLYQRYQQWSLSAEQrYL 551
                                             ******************************************************99555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (536 nodes)
Target sequences:                          1  (569 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: 9.78
//
[ok]

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:

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