GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Lactobacillus oryzae SG293

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_034527995.1 LOSG293_RS05510 acetate kinase

Query= BRENDA::Q9F1X7
         (397 letters)



>NCBI__GCF_000740055.1:WP_034527995.1
          Length = 395

 Score =  526 bits (1354), Expect = e-154
 Identities = 255/394 (64%), Positives = 325/394 (82%), Gaps = 1/394 (0%)

Query: 1   MSKIIAVNAGSSTLKFKLYEMPEENVLAEGVIERIALPASHVEIKYGDGKKYEKTTDVKN 60
           M K +AVNAGSSTLKFKL++MPEE  ++ GV+ERI L  S V IKYGDG+K+E+T D+++
Sbjct: 1   MGKSMAVNAGSSTLKFKLFQMPEETEISSGVVERIGLKDSLVLIKYGDGQKFEETLDIES 60

Query: 61  HEQAIQILLDQLLDLDIIKEYSEINGVGHRVVAGGEYFDKSVVITPDVLKKIESLTELAP 120
           HEQAIQI+LDQLLDL IIK+Y+EI GVGHRVVAGGE F  S +I   V+++IESL E AP
Sbjct: 61  HEQAIQIMLDQLLDLKIIKDYNEITGVGHRVVAGGELFSDSALIDDKVIEQIESLAEYAP 120

Query: 121 LHEPANVLGIKAFKKVLPDIISVAVFDTAFHATLPEKNFLYSLPYEYYEKYSARKYGFHG 180
           LH PA  +GI+AFKK+LPDI SVAVFDT+FH ++P  N++Y LPYEYYEK+ ARKYG HG
Sbjct: 121 LHNPAEAMGIRAFKKLLPDIPSVAVFDTSFHTSMPAVNYMYPLPYEYYEKFGARKYGAHG 180

Query: 181 IGNRYVSQRAAELLGKPAEDLKMIITHLGAGASICPVKNGKSFDTSMGFTPVTGITMATR 240
             +RYV+ +AAE+LG+P EDLK++  H+GAGASI  ++NGKS+DTSMGFTP+TG+ MATR
Sbjct: 181 TSHRYVAHKAAEMLGRPLEDLKLVTLHIGAGASITAIQNGKSYDTSMGFTPLTGVMMATR 240

Query: 241 SGDVDPSLLAYVMEKEGMTDINEMIKVLNTKSGLLGISGVSADMREVEAAQATNPRAKVA 300
           +GD+D SL+ Y+MEK  +  ++EMI +LN KSGL+G+SGVSADMR+VE  Q  N RAK+A
Sbjct: 241 TGDIDVSLVKYLMEKLNI-GMDEMIDILNHKSGLIGVSGVSADMRDVEGVQDKNDRAKLA 299

Query: 301 REIYVNRIIRYVGAYLAEMGGADAIVFTAGVGENSITIRKEVAEGLNYFGIGVDNEKNDV 360
           R++Y+ RI+RYVG Y+AE+ G DAIVFTAGVGEN  TIR+EVA+ L +FGI VD EKN +
Sbjct: 300 RDMYIERIVRYVGQYIAELDGVDAIVFTAGVGENDFTIRQEVADKLGFFGIKVDPEKNHI 359

Query: 361 RGVVRDISAKDSKIKTLLVPTDEELMIVRDVQTL 394
           RGV RD+SA D+ +KTLL+PT+EELMIVRD++ L
Sbjct: 360 RGVQRDLSADDATVKTLLIPTNEELMIVRDIERL 393


Lambda     K      H
   0.316    0.135    0.372 

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: 479
Number of extensions: 15
Number of successful extensions: 2
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
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: 50 (23.9 bits)

Align candidate WP_034527995.1 LOSG293_RS05510 (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.2205888.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.5e-155  503.8   0.4   1.7e-155  503.6   0.4    1.0  1  NCBI__GCF_000740055.1:WP_034527995.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000740055.1:WP_034527995.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  503.6   0.4  1.7e-155  1.7e-155       6     404 ..       4     394 ..       1     395 [] 0.98

  Alignments for each domain:
  == domain 1  score: 503.6 bits;  conditional E-value: 1.7e-155
                             TIGR00016   6 ilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkd 78 
                                            + +naGss lkf+l+++ + e+ + sg+veri l+++ + ++  +++k ee+l+ie+he+a++ +l++l  d
  NCBI__GCF_000740055.1:WP_034527995.1   4 SMAVNAGSSTLKFKLFQMPE-ETEISSGVVERIGLKDSLVLIKYGDGQKFEETLDIESHEQAIQIMLDQLL-D 74 
                                           589****************6.8888****************999999************************.8 PP

                             TIGR00016  79 kkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvav 151
                                            ki+k+ +ei+ +GHRvv Gge f++s++++d+v+++i+ ++e+APlHnpae+ gi+a++  k l++ + vav
  NCBI__GCF_000740055.1:WP_034527995.1  75 LKIIKDYNEITGVGHRVVAGGELFSDSALIDDKVIEQIESLAEYAPLHNPAEAMGIRAFK--KLLPDIPSVAV 145
                                           ************************************************************..889999***** PP

                             TIGR00016 152 FDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavk 224
                                           FDt+fH+ +p  +y+Y+lPy++y+++g R+YG+HGtsh+yv+++aa++l++pl+dl+l+++H+G Gas++a++
  NCBI__GCF_000740055.1:WP_034527995.1 146 FDTSFHTSMPAVNYMYPLPYEYYEKFGARKYGAHGTSHRYVAHKAAEMLGRPLEDLKLVTLHIGAGASITAIQ 218
                                           ************************************************************************* PP

                             TIGR00016 225 nGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkke 297
                                           nGks+dtsmG+tPL G++m tR+GdiD ++++yl+e+l+  +de+ ++ln ksGl+g+sg+s+D+Rd++  + 
  NCBI__GCF_000740055.1:WP_034527995.1 219 NGKSYDTSMGFTPLTGVMMATRTGDIDVSLVKYLMEKLNIGMDEMIDILNHKSGLIGVSGVSADMRDVEGVQ- 290
                                           ********************************************************************9887. PP

                             TIGR00016 298 egneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaars 370
                                           ++n++aklA ++y++Ri +y+g+yia+l+g +DaivFt+G+Gen+ ++r++v +kl ++G+k+d+e+n+   +
  NCBI__GCF_000740055.1:WP_034527995.1 291 DKNDRAKLARDMYIERIVRYVGQYIAELDG-VDAIVFTAGVGENDFTIRQEVADKLGFFGIKVDPEKNH--IR 360
                                           8899************************88.**************************************..77 PP

                             TIGR00016 371 gkesvisteeskvkvlviptneelviaeDalrla 404
                                           g ++ +s ++++vk l iptneel+i++D+ rl 
  NCBI__GCF_000740055.1:WP_034527995.1 361 GVQRDLSADDATVKTLLIPTNEELMIVRDIERLK 394
                                           888889************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (395 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: 16.82
//
[ok]

This GapMind analysis is from Sep 24 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