Alignments for a candidate for araB in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for araB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Ribulokinase (EC 2.7.1.16) (characterized)
to candidate Echvi_0515 Echvi_0515 L-ribulokinase

Query= reanno::Cola:Echvi_0515
         (562 letters)



>FitnessBrowser__Cola:Echvi_0515
          Length = 562

 Score = 1131 bits (2926), Expect = 0.0
 Identities = 562/562 (100%), Positives = 562/562 (100%)

Query: 1   MNDKFVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCDPVNNQFRQHPLDHL 60
           MNDKFVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCDPVNNQFRQHPLDHL
Sbjct: 1   MNDKFVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCDPVNNQFRQHPLDHL 60

Query: 61  EGLEETIREVIKESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLW 120
           EGLEETIREVIKESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLW
Sbjct: 61  EGLEETIREVIKESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLW 120

Query: 121 KDHTAIKEADEINELARTWGGEDYTKYEGGIYSSEWFWAKILHVIREDDAVAQAAYSWME 180
           KDHTAIKEADEINELARTWGGEDYTKYEGGIYSSEWFWAKILHVIREDDAVAQAAYSWME
Sbjct: 121 KDHTAIKEADEINELARTWGGEDYTKYEGGIYSSEWFWAKILHVIREDDAVAQAAYSWME 180

Query: 181 HCDVITAELIGADNPLDVKRSRCAAGHKALWHESWDGLPPKEFLSKLDPRLADLRDRLYT 240
           HCDVITAELIGADNPLDVKRSRCAAGHKALWHESWDGLPPKEFLSKLDPRLADLRDRLYT
Sbjct: 181 HCDVITAELIGADNPLDVKRSRCAAGHKALWHESWDGLPPKEFLSKLDPRLADLRDRLYT 240

Query: 241 ETFTSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTENTLVKVMGTSTCDI 300
           ETFTSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTENTLVKVMGTSTCDI
Sbjct: 241 ETFTSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTENTLVKVMGTSTCDI 300

Query: 301 MVATHEAIGDNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVVKPTAALIRAS 360
           MVATHEAIGDNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVVKPTAALIRAS
Sbjct: 301 MVATHEAIGDNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVVKPTAALIRAS 360

Query: 361 NVLDEEKKEALIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVM 420
           NVLDEEKKEALIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVM
Sbjct: 361 NVLDEEKKEALIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVM 420

Query: 421 GLNMGTDAARVFKALVESICFGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADV 480
           GLNMGTDAARVFKALVESICFGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADV
Sbjct: 421 GLNMGTDAARVFKALVESICFGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADV 480

Query: 481 LNMPIKIATSDQAPALGAAMYASVAAGIHPTTEAAIAAMTNGFDKVYEPIPENVEVYKAL 540
           LNMPIKIATSDQAPALGAAMYASVAAGIHPTTEAAIAAMTNGFDKVYEPIPENVEVYKAL
Sbjct: 481 LNMPIKIATSDQAPALGAAMYASVAAGIHPTTEAAIAAMTNGFDKVYEPIPENVEVYKAL 540

Query: 541 YAKYAEFGAFVEGQTSPVLADQ 562
           YAKYAEFGAFVEGQTSPVLADQ
Sbjct: 541 YAKYAEFGAFVEGQTSPVLADQ 562


Lambda     K      H
   0.316    0.133    0.398 

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: 1233
Number of extensions: 26
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: 562
Length of database: 562
Length adjustment: 36
Effective length of query: 526
Effective length of database: 526
Effective search space:   276676
Effective search space used:   276676
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate Echvi_0515 Echvi_0515 (L-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.24428.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   7.4e-189  614.8   1.9   8.4e-189  614.6   1.9    1.0  1  lcl|FitnessBrowser__Cola:Echvi_0515  Echvi_0515 L-ribulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_0515  Echvi_0515 L-ribulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  614.6   1.9  8.4e-189  8.4e-189       1     531 [.       4     552 ..       4     558 .. 0.96

  Alignments for each domain:
  == domain 1  score: 614.6 bits;  conditional E-value: 8.4e-189
                            TIGR01234   1 ayaiGvdfGtlsgralvvdvatGeelaaavkeyrravvdevldkteaklPadyalqhPadyievleaaikevla 74 
                                          +++iG+d+G++s+ra++v+  +Ge  ++ v +y+r++ ++ +d   +   +++++qhP d++e le +i+ev++
  lcl|FitnessBrowser__Cola:Echvi_0515   4 KFVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCD--PV---NNQFRQHPLDHLEGLEETIREVIK 72 
                                          589****************************************..33...89********************** PP

                            TIGR01234  75 elgvdpadvvGiGvdftastivpidsdGnvlallpefaeePhayvklWkdhaaqeeadrinrlaeaeGevflsr 148
                                          e gv   ++ Gi vd t+s ++++d +G++lal pefae+P+a+++lWkdh+a +ead+in+la+  G  ++++
  lcl|FitnessBrowser__Cola:Echvi_0515  73 ESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLWKDHTAIKEADEINELARTWGGEDYTK 146
                                          ************************************************************************** PP

                            TIGR01234 149 yg.GlisseWlfakvlqiaeedpeiyeaadrwieaadWivaqlsG.....dlkrsrctaGykalwseskg.yPs 215
                                          y  G++sseW++ak+l++++ed ++++aa +w+e +d i+a l G     d+krsrc+aG+kalw+es+  +P+
  lcl|FitnessBrowser__Cola:Echvi_0515 147 YEgGIYSSEWFWAKILHVIREDDAVAQAAYSWMEHCDVITAELIGadnplDVKRSRCAAGHKALWHESWDgLPP 220
                                          *889*****************************************************************66*** PP

                            TIGR01234 216 asfleelnPslkrivkdkletdigsvgekaGtltekaakllGlpegvvvavgnvdahvsaaaagiaePgklvki 289
                                          ++fl +l+P l+  ++d+l t++++ + +aG l++++ak+lGl   +v+avg++dah +a++ +++e + lvk+
  lcl|FitnessBrowser__Cola:Echvi_0515 221 KEFLSKLDPRLAD-LRDRLYTETFTSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTE-NTLVKV 292
                                          ***********87.79************************************************766.89**** PP

                            TIGR01234 290 iGtstcdvllgekl....ravkGicGvvdggivpGfiGyeaGqsavGdifaWfvkvl............vppel 347
                                          +Gtstcd++++ +     + vkGicG+vdg+++pG +G+eaGqs++Gd+ aWf + +            v  e 
  lcl|FitnessBrowser__Cola:Echvi_0515 293 MGTSTCDIMVATHEaigdNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVvkptaalirasnVLDEE 366
                                          ***********998789899*********************************99999999****999944444 PP

                            TIGR01234 348 kee..akekqlqllealsekaakqesgehglvaldWfnGnrsvlvdarlkGvlvgltlatkaeelyralveata 419
                                          k+e  ++e + qll +lse a + +  e  +valdW nG+r++ +++ lkG ++gl++ t+a  +++alve+  
  lcl|FitnessBrowser__Cola:Echvi_0515 367 KKEalIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVMGLNMGTDAARVFKALVESIC 440
                                          444125777889************************************************************** PP

                            TIGR01234 420 fGtrmivetfkesGvaveellaaGGiaeknplvmqiyadvlnlplkivasdqapalGaaifaavaageyadipk 493
                                          fG++ iv+ f+e+Gva++ ++ +GG+a+k +lvmq +advln+p+ki++sdqapalGaa++a+vaag +   + 
  lcl|FitnessBrowser__Cola:Echvi_0515 441 FGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADVLNMPIKIATSDQAPALGAAMYASVAAGIHPTTEA 514
                                          ************************************************************************** PP

                            TIGR01234 494 aaakmgsavektltPisenaaryeklyaeykeladyfg 531
                                          a a m++  +k ++Pi+en+++y++lya+y e+  +++
  lcl|FitnessBrowser__Cola:Echvi_0515 515 AIAAMTNGFDKVYEPIPENVEVYKALYAKYAEFGAFVE 552
                                          ********************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (536 nodes)
Target sequences:                          1  (562 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.85
//
[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)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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