Alignments for a candidate for ackA in Klebsiella michiganensis M5al

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.20151.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: 00:00:00.01
# Mc/sec: 10.85
//
[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:

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