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

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.25243.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 9.32
//
[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