GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Luteimonas huabeiensis HB2

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_024890056.1 Z164_RS0107325 acetate/propionate family kinase

Query= curated2:Q6N143
         (398 letters)



>NCBI__GCF_000559025.1:WP_024890056.1
          Length = 405

 Score =  347 bits (889), Expect = e-100
 Identities = 195/401 (48%), Positives = 251/401 (62%), Gaps = 13/401 (3%)

Query: 4   VLLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGH-RPHFKVVNSDGSTRYDTYLP 62
           ++LVLN GSSSIKFAL+ A   P A   +  G +  +G   P F      G   +   L 
Sbjct: 8   LILVLNCGSSSIKFALFAADVHPLARTPLWNGKVQGIGGPAPDF---GETGVAPHRVELD 64

Query: 63  EGTSHDDAMAVLIGWIETTFPEHRLSAVGHRVVHGGALFDGPVDVTPEVIAQLRAFDRLA 122
            G  H  A+ V+   I T     R+ AV HRVVHGG  +  P  V  + +A LR++  LA
Sbjct: 65  AGHPHSAALQVIRERIRTRLNGRRVVAVAHRVVHGGTKYSAPTRVDAQTLADLRSYVPLA 124

Query: 123 PLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVRRYGFHG 182
           PLHQP  + A++ L + HP + Q+ACFDTAFH  LP+V     LP     +G+RRYGFHG
Sbjct: 125 PLHQPFALEAMDILLREHPDIVQVACFDTAFHRTLPKVEQLLPLPHAAWARGLRRYGFHG 184

Query: 183 LSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALDGLMMGSR 242
           LSYEY+A  LP+  G  +A GRV+VAHLG+GAS+CAM    S+ATTMGF+ALDGLMMG+R
Sbjct: 185 LSYEYMAAALPERHGD-LASGRVIVAHLGSGASLCAMRGLHSVATTMGFSALDGLMMGTR 243

Query: 243 CGELDPGVVLYLLEEKSMTAREIEDLLYRESGLLGVSGISDDMRTLLA------SDDPHA 296
            G LDPG V+YL+E + ++  ++  +LY ESGLLGVSGIS + R LL        D   A
Sbjct: 244 TGALDPGAVIYLMEIEKLSLEQVAHILYHESGLLGVSGISAEPRVLLQKETGNDEDAARA 303

Query: 297 CEAIELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPDA 356
            +A+ L+V RI RE+G+L A LGGLD LVFT G+GEH+ EIRRRVCE   +L + LDP A
Sbjct: 304 RDALSLYVRRIVREIGALVAVLGGLDLLVFTAGVGEHSPEIRRRVCESLGFLPLRLDPPA 363

Query: 357 NASLSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRLADGG 397
           N  L+ A  ISA DS+V     PT+E+ + AR    L   G
Sbjct: 364 N--LANAPVISAADSEVIVGVEPTNEEWVAARAALTLCRTG 402


Lambda     K      H
   0.321    0.137    0.413 

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: 520
Number of extensions: 21
Number of successful extensions: 5
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: 398
Length of database: 405
Length adjustment: 31
Effective length of query: 367
Effective length of database: 374
Effective search space:   137258
Effective search space used:   137258
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_024890056.1 Z164_RS0107325 (acetate/propionate family 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.2793428.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-102  328.2   0.0   3.6e-102  328.0   0.0    1.0  1  NCBI__GCF_000559025.1:WP_024890056.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000559025.1:WP_024890056.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.0   0.0  3.6e-102  3.6e-102       4     404 ..       7     399 ..       4     400 .. 0.92

  Alignments for each domain:
  == domain 1  score: 328.0 bits;  conditional E-value: 3.6e-102
                             TIGR00016   4 kkilvlnaGssslkfalldaen...sekvllsglverikleeariktvedgekkeeeklaiedheeavkklln 73 
                                           ++ilvln+Gsss+kfal+ a     +++ l++g v+ i  +            ++ e  a + h++a++ + +
  NCBI__GCF_000559025.1:WP_024890056.1   7 SLILVLNCGSSSIKFALFAADVhplARTPLWNGKVQGIGGPAPDFGETG-VAPHRVELDAGHPHSAALQVIRE 78 
                                           78****************98765566777*********99888544333.3456778889999********** PP

                             TIGR00016  74 tlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllka 146
                                           ++ +    + +   + ++ HRvvhGg+k++  + v++++l++++  ++lAPlH p +le+++++l   ++++ 
  NCBI__GCF_000559025.1:WP_024890056.1  79 RIRT----RLNGRRVVAVAHRVVHGGTKYSAPTRVDAQTLADLRSYVPLAPLHQPFALEAMDILL--REHPDI 145
                                           **97....5677899************************************************99..999999 PP

                             TIGR00016 147 knvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGas 219
                                            +va+FDtafH+t+p+   l +lP+ ++   g+RrYGfHG+s++y++  + +  +  l++ ++iv+HlG Gas
  NCBI__GCF_000559025.1:WP_024890056.1 146 VQVACFDTAFHRTLPKVEQLLPLPHAAWA-RGLRRYGFHGLSYEYMAAALPERHGD-LASGRVIVAHLGSGAS 216
                                           ************************88886.69*********************998.99************** PP

                             TIGR00016 220 vsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdi 292
                                           ++a++  +s+ t+mG+  L+Gl+mGtR+G +Dp+++ yl+e ++lsl+++ ++l  +sGllg+sg+s++ R++
  NCBI__GCF_000559025.1:WP_024890056.1 217 LCAMRGLHSVATTMGFSALDGLMMGTRTGALDPGAVIYLMEIEKLSLEQVAHILYHESGLLGVSGISAEPRVL 289
                                           ************************************************************************* PP

                             TIGR00016 293 ldkke...egneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldl 362
                                           l+k +   e   +a+ Al++yv Ri + ig+ +a l g lD +vFt+G+Ge + e+r++v+e+l +l l+ld+
  NCBI__GCF_000559025.1:WP_024890056.1 290 LQKETgndEDAARARDALSLYVRRIVREIGALVAVLGG-LDLLVFTAGVGEHSPEIRRRVCESLGFLPLRLDP 361
                                           *99863225555677899******************76.********************************** PP

                             TIGR00016 363 elnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                             n      +  vis  +s+v v v ptnee+v a+ al l+
  NCBI__GCF_000559025.1:WP_024890056.1 362 PANL----ANAPVISAADSEVIVGVEPTNEEWVAARAALTLC 399
                                           *999....7789**********************99988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (405 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: 00:00:00.00
# Mc/sec: 17.59
//
[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