GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Dinoroseobacter shibae DFL-12

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate 3608653 Dshi_5006 hypothetical protein (NCBI)

Query= curated2:Q6N143
         (398 letters)



>FitnessBrowser__Dino:3608653
          Length = 385

 Score =  283 bits (723), Expect = 8e-81
 Identities = 172/394 (43%), Positives = 230/394 (58%), Gaps = 20/394 (5%)

Query: 2   SDVLLVLNAGSSSIKFALYEAHTEPTADHLICEGGIGSLGHRPHFKVVNSDGSTRYDTYL 61
           SD++LVLNAGSSS+KFAL+   T   A+HL   G   S+G     K+    G+      L
Sbjct: 7   SDLILVLNAGSSSLKFALF---TPALAEHLT--GQAESIGGPGRLKI----GARSASCDL 57

Query: 62  PEGTSHDDAMAVLIGWIETT-FPEHRLSAVGHRVVHGGALFDGPVDVTPEVIAQLRAFDR 120
           P+   H  A+A ++  + T       L AV HRVVHGG     PV +TP   +++ A   
Sbjct: 58  PD---HGAALAAILEALATRGITASHLKAVAHRVVHGGVRLTAPVRITPATRSEIAACSA 114

Query: 121 LAPLHQPHNVSAIEALAKLHPSLPQIACFDTAFHHRLPEVATAFALPRELTEQGVRRYGF 180
           LAPLH PHN++AI+ +  L P +PQ A FDTAFH   PEVA  + LP      G+RRYGF
Sbjct: 115 LAPLHNPHNLAAIDRITALMPDVPQCASFDTAFHASNPEVALRYGLPDTAETAGLRRYGF 174

Query: 181 HGLSYEYIAGRLPDVAGQAVADGRVVVAHLGAGASMCAMLRCRSIATTMGFTALDGLMMG 240
           HG SY  +      V G A+ D R++  HLG+GAS+CA+   RS+ATTMG++ L+GL M 
Sbjct: 175 HGQSYAAMVDSWSRVTGAALPD-RLLAFHLGSGASICAIRDGRSVATTMGYSPLEGLTMA 233

Query: 241 SRCGELDPGVVLYLLEEKSMT-AREIEDLLYRESGLLGVSGISDDMRTLLASDDPHACEA 299
           +R G +D   VL L E+  +  AR I   L  ESGL G+SG   DMRTL+ASD P A  A
Sbjct: 234 TRSGSIDGNAVLKLAEDHGIARARRI---LNNESGLAGLSGGLSDMRTLMASDRPEAGFA 290

Query: 300 IELFVYRIARELGSLAAALGGLDALVFTGGIGEHASEIRRRVCEQAAWLGVTLDPDANAS 359
           ++ FVY   R   SL A LGG + + FTGGIGE+A+EIR R+     W+G  +DP+ANA 
Sbjct: 291 VDHFVYWAVRHASSLLAPLGGTETIAFTGGIGENAAEIRARIVAGLHWIGAEIDPEANA- 349

Query: 360 LSGAGRISAPDSKVSAWAIPTDEDLMIARHVWRL 393
             G   + +  S    + IP +E+ M+A    R+
Sbjct: 350 -EGQTALHSAASATGIYIIPAEEERMLAADALRV 382


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: 478
Number of extensions: 26
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: 385
Length adjustment: 31
Effective length of query: 367
Effective length of database: 354
Effective search space:   129918
Effective search space used:   129918
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 3608653 Dshi_5006 (hypothetical protein (NCBI))
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.1056.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
    4.7e-94  301.3   0.0    5.4e-94  301.1   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608653  Dshi_5006 hypothetical protein (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608653  Dshi_5006 hypothetical protein (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.1   0.0   5.4e-94   5.4e-94       3     403 ..       7     382 ..       5     384 .. 0.93

  Alignments for each domain:
  == domain 1  score: 301.1 bits;  conditional E-value: 5.4e-94
                         TIGR00016   3 skkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdk 79 
                                       s +ilvlnaGssslkfal+  + +e++   g +e i  ++  +   + g   +++  + +dh +a++++l++l + +
  lcl|FitnessBrowser__Dino:3608653   7 SDLILVLNAGSSSLKFALFTPALAEHL--TGQAESIGGPGR-L---KIG--ARSASCDLPDHGAALAAILEALAT-R 74 
                                       678*******************77766..9*******9999.3...334..4568899****************6.6 PP

                         TIGR00016  80 kilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtaf 156
                                        i  + s+++++ HRvvhGg ++t  v +t  + ++i+  s lAPlHnp +l +i+ ++    ++++++ a FDtaf
  lcl|FitnessBrowser__Dino:3608653  75 GI--TASHLKAVAHRVVHGGVRLTAPVRITPATRSEIAACSALAPLHNPHNLAAIDRIT--ALMPDVPQCASFDTAF 147
                                       66..5689***************************************************..889999********** PP

                         TIGR00016 157 HqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsm 233
                                       H   pe a  Y+lP +  +  g+RrYGfHG s+  + ++ +++ + +l d +l+  HlG Gas++a+++G+s+ t+m
  lcl|FitnessBrowser__Dino:3608653 148 HASNPEVALRYGLP-DTAETAGLRRYGFHGQSYAAMVDSWSRVTGAALPD-RLLAFHLGSGASICAIRDGRSVATTM 222
                                       **************.788899*********************99997765.899*********************** PP

                         TIGR00016 234 GltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvy 310
                                       G  PLeGl m tRsG+iD  ++  lae +g +     ++ln +sGl g+sg  sD+R++++     + ea  A++ +
  lcl|FitnessBrowser__Dino:3608653 223 GYSPLEGLTMATRSGSIDGNAVLKLAEDHGIA--RARRILNNESGLAGLSGGLSDMRTLMASD---RPEAGFAVDHF 294
                                       **********************9999988765..668**********************9877...7789******* PP

                         TIGR00016 311 vhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlv 387
                                       v+   ++ ++ +a l g  ++i FtgGiGenaae+r++++ +l+ +G ++d+e n     + ++ + +  s++ +++
  lcl|FitnessBrowser__Dino:3608653 295 VYWAVRHASSLLAPLGG-TETIAFTGGIGENAAEIRARIVAGLHWIGAEIDPEANA----EGQTALHSAASATGIYI 366
                                       ***************77.9***********************************99....55666777999****** PP

                         TIGR00016 388 iptneelviaeDalrl 403
                                       ip +ee ++a Dalr+
  lcl|FitnessBrowser__Dino:3608653 367 IPAEEERMLAADALRV 382
                                       *************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (385 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 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.10
//
[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