GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Klebsiella michiganensis M5al

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate BWI76_RS20235 BWI76_RS20235 acetate kinase

Query= BRENDA::P63411
         (400 letters)



>FitnessBrowser__Koxy:BWI76_RS20235
          Length = 400

 Score =  773 bits (1997), Expect = 0.0
 Identities = 388/400 (97%), Positives = 393/400 (98%)

Query: 1   MSSKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAG 60
           MSSKLVLVLNCGSSSLKFAI+DAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEA LGAG
Sbjct: 1   MSSKLVLVLNCGSSSLKFAILDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAELGAG 60

Query: 61  AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFA 120
           AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVID+SVIQGIKDSASFA
Sbjct: 61  AAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDDSVIQGIKDSASFA 120

Query: 121 PLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180
           PLHNPAHLIGIAEALKSFP LKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG
Sbjct: 121 PLHNPAHLIGIAEALKSFPNLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYG 180

Query: 181 AHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240
           AHGTSHFYVTQEAAK+LNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM
Sbjct: 181 AHGTSHFYVTQEAAKVLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVM 240

Query: 241 GTRSGDIDPAIIFHLHDTLGMSVDQINKMLTKESGLLGLTEVTSDCRYVEDNYATKEDAK 300
           GTRSGDIDPAIIFHLHD LGMSVD INKMLTKESGLLGLTEVTSDCRYVEDNY  K DAK
Sbjct: 241 GTRSGDIDPAIIFHLHDALGMSVDAINKMLTKESGLLGLTEVTSDCRYVEDNYQEKADAK 300

Query: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360
           RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER
Sbjct: 301 RAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHER 360

Query: 361 NLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
           NLAARFGKSGFINKEGTRPA+VIPTNEELVIAQDA+RLTA
Sbjct: 361 NLAARFGKSGFINKEGTRPAIVIPTNEELVIAQDANRLTA 400


Lambda     K      H
   0.318    0.134    0.384 

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: 628
Number of extensions: 9
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: 400
Length of database: 400
Length adjustment: 31
Effective length of query: 369
Effective length of database: 369
Effective search space:   136161
Effective search space used:   136161
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate BWI76_RS20235 BWI76_RS20235 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

# 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/TIGR00016.hmm
# target sequence database:        /tmp/gapView.29676.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00016  [M=405]
Accession:   TIGR00016
Description: ackA: acetate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.3e-189  614.3   0.0   4.7e-189  614.2   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS20235  BWI76_RS20235 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS20235  BWI76_RS20235 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  614.2   0.0  4.7e-189  4.7e-189       1     404 [.       1     399 [.       1     400 [] 0.98

  Alignments for each domain:
  == domain 1  score: 614.2 bits;  conditional E-value: 4.7e-189
                               TIGR00016   1 mkskkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkl 71 
                                             m+sk++lvln+Gssslkfa+lda n++++ lsgl+e+++l+earik+++dg+k+e+e  a ++h+ea++++
  lcl|FitnessBrowser__Koxy:BWI76_RS20235   1 MSSKLVLVLNCGSSSLKFAILDAVNGDEY-LSGLAECFHLPEARIKWKMDGSKQEAELGAGAAHSEALNFI 70 
                                             57899************************.9**************************************** PP

                               TIGR00016  72 lntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkv 142
                                             +nt+ ++k   ++++++++iGHR+vhGgek+t+sv+++d+v+++ikd +++APlHnpa+l+gi ++lk+++
  lcl|FitnessBrowser__Koxy:BWI76_RS20235  71 VNTILAQK--PELSAQLTAIGHRIVHGGEKYTSSVVIDDSVIQGIKDSASFAPLHNPAHLIGIAEALKSFP 139
                                             *****866..99*********************************************************** PP

                               TIGR00016 143 llkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcH 213
                                              lk+knvavFDtafHqt+pee+ylYalPyslyke+gvRrYG+HGtsh yvtq+aak+lnkp+++ln+i+cH
  lcl|FitnessBrowser__Koxy:BWI76_RS20235 140 NLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYGAHGTSHFYVTQEAAKVLNKPVEELNIITCH 210
                                             *********************************************************************** PP

                               TIGR00016 214 lGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisg 284
                                             lGnG+svsa++nGk++dtsmGltPLeGlvmGtRsGdiDpaii++l++ lg+s+d+i+++l+k+sGllg+++
  lcl|FitnessBrowser__Koxy:BWI76_RS20235 211 LGNGGSVSAIRNGKCVDTSMGLTPLEGLVMGTRSGDIDPAIIFHLHDALGMSVDAINKMLTKESGLLGLTE 281
                                             *********************************************************************** PP

                               TIGR00016 285 lssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklev 355
                                             ++sD+R+++d++ +++ +ak+A++vy+hR+akyig+y+a ++g+lDa+vFtgGiGenaa+vrel+l kl v
  lcl|FitnessBrowser__Koxy:BWI76_RS20235 282 VTSDCRYVEDNY-QEKADAKRAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGV 351
                                             ************.6667****************************************************** PP

                               TIGR00016 356 lGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                             lG+++d+e+n aar+gk+++i+ +e++  ++viptneelvia+Da rl+
  lcl|FitnessBrowser__Koxy:BWI76_RS20235 352 LGFEVDHERNLAARFGKSGFIN-KEGTRPAIVIPTNEELVIAQDANRLT 399
                                             *********************9.89999*****************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (400 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.85
//
[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