Alignments for a candidate for araB in Klebsiella michiganensis M5al

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.2065611.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 35.49
//
[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:

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