GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ackA in Synechococcus elongatus PCC 7942

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate Synpcc7942_2079 Synpcc7942_2079 acetate kinase

Query= curated2:Q8YU00
         (405 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_2079 Synpcc7942_2079 acetate
           kinase
          Length = 393

 Score =  337 bits (864), Expect = 4e-97
 Identities = 189/405 (46%), Positives = 256/405 (63%), Gaps = 19/405 (4%)

Query: 1   MKVLILNAGSSSQKSCLYEIPDDALLSEAPQPLWEGKVNWTQDRSVAEIEVKTARGETLH 60
           +++L  NAGSSS K   +EI   A   E   P+W+ +++W  DR+       T  G+ + 
Sbjct: 1   LQLLTFNAGSSSYKLSGFEITTAA---EQTDPVWQVQIDWKTDRAAT----LTQPGQPV- 52

Query: 61  ESIYGDSRQAHVTYMLYTLSRGATKVIGQLSEIDVVGHRVVHGGQNYRHSVIITEEVKQA 120
           + +    R+A +   L TL           S I  V HRVVHGGQ    +V+ T E+K  
Sbjct: 53  QMLDSSDRRAWLEIALETLP--------DRSAIAAVVHRVVHGGQQQAPAVV-TPELKAT 103

Query: 121 IAKLSNLAPAHNPAALEGIEAIEKSLG-DVPQVAVFDTGFHATLPDAAAIYPGPFEWVEQ 179
           IA  +NLAP HNP  L GIE +E+  G  +PQ+AVFDT FH  +P AAAIY GP+ W EQ
Sbjct: 104 IAAAANLAPLHNPLNLAGIEQMEQLFGLAMPQIAVFDTAFHQQMPVAAAIYGGPYHWWEQ 163

Query: 180 GIRRYGFHGISHQYCSARAAQILGRDLASLRIITCHLGNGCSLAAIKNGRSIDTTMGFTP 239
           G RRYGFHGISHQY + R AQ+  R L++L+++T HLGNGCSLAAI+NG S+DT+MGF+P
Sbjct: 164 GYRRYGFHGISHQYLAERCAQLSDRSLSNLQLVTAHLGNGCSLAAIRNGHSVDTSMGFSP 223

Query: 240 LDGLMMGSRSGAIDPGIIVHLMRQSDYSAERLDYVLNKASGLRGISGVSSDLPQVIEAIT 299
           L+GL+MGSRSG +DPG+++HL++Q D S  +L  VLN+ SGL G+SG S+D+  +  A  
Sbjct: 224 LEGLVMGSRSGTVDPGLLLHLLQQPDCSPSQLSTVLNQQSGLLGLSGRSNDVRALAIAAD 283

Query: 300 QGNYRAQLAWDMYVHRLRSGIGSMLASLGGLDVLVFTAGVGEKSAGIRQAACEAFGFLGL 359
            G+ R+QLA   + H LR  +G+MLASL  LD LVF  G+GE    +  A CE F  + +
Sbjct: 284 AGDQRSQLALAAFTHSLRRHLGAMLASLTRLDALVFAGGIGENYRSLWPAVCEHFAGMPI 343

Query: 360 KLDPEKNQNKPVDIDIATADSTVRVLVIHTQEDWAIAQQCWHLLK 404
           +LDPE       D  I+T DS + V VIH++EDW + Q    LL+
Sbjct: 344 RLDPEA-MAVAGDRRISTPDSAITVWVIHSREDWQMVQLALPLLR 387


Lambda     K      H
   0.319    0.135    0.400 

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: 428
Number of extensions: 15
Number of successful extensions: 6
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: 405
Length of database: 393
Length adjustment: 31
Effective length of query: 374
Effective length of database: 362
Effective search space:   135388
Effective search space used:   135388
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate Synpcc7942_2079 Synpcc7942_2079 (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.32177.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     9e-110  353.1   0.0     1e-109  352.9   0.0    1.0  1  lcl|FitnessBrowser__SynE:Synpcc7942_2079  Synpcc7942_2079 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__SynE:Synpcc7942_2079  Synpcc7942_2079 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  352.9   0.0    1e-109    1e-109       6     400 ..       3     382 ..       1     387 [. 0.91

  Alignments for each domain:
  == domain 1  score: 352.9 bits;  conditional E-value: 1e-109
                                 TIGR00016   6 ilvlnaGssslkfalldaensekv...llsglverikleeariktvedgekkeeeklaiedheeavkkl 71 
                                               +l  naGsss k + ++ +++ +    +++  +++ +    r  t+++   +  ++l+ +d+++ ++  
  lcl|FitnessBrowser__SynE:Synpcc7942_2079   3 LLTFNAGSSSYKLSGFEITTAAEQtdpVWQVQIDWKT---DRAATLTQP-GQPVQMLDSSDRRAWLEIA 67 
                                               7899*********999999866652335555555543...333444444.4667889999999999999 PP

                                 TIGR00016  72 lntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlkl 140
                                               l+tl        + s ia++ HRvvhGg++ + + +vt e  + i+ +++lAPlHnp +l gie++ +l
  lcl|FitnessBrowser__SynE:Synpcc7942_2079  68 LETLP-------DRSAIAAVVHRVVHGGQQQAPA-VVTPELKATIAAAANLAPLHNPLNLAGIEQMEQL 128
                                               99999.......4799************998766.689*****************************88 PP

                                 TIGR00016 141 kvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnl 209
                                               + l   +++avFDtafHq +p  a++Y+ Py++++ +g RrYGfHG+sh+y+++r a+l +++l +l+l
  lcl|FitnessBrowser__SynE:Synpcc7942_2079 129 FGLAM-PQIAVFDTAFHQQMPVAAAIYGGPYHWWE-QGYRRYGFHGISHQYLAERCAQLSDRSLSNLQL 195
                                               77665.***************************96.699****************************** PP

                                 TIGR00016 210 ivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksG 278
                                               +++HlGnG s++a++nG+s+dtsmG+ PLeGlvmG+RsG +Dp+++ +l ++ + s +++ ++ln++sG
  lcl|FitnessBrowser__SynE:Synpcc7942_2079 196 VTAHLGNGCSLAAIRNGHSVDTSMGFSPLEGLVMGSRSGTVDPGLLLHLLQQPDCSPSQLSTVLNQQSG 264
                                               ********************************************************************* PP

                                 TIGR00016 279 llgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevre 347
                                               llg+sg s+D+R +  + ++g+++++lAl  ++h +++++g+++asl  +lDa+vF gGiGen  ++  
  lcl|FitnessBrowser__SynE:Synpcc7942_2079 265 LLGLSGRSNDVRALAIAADAGDQRSQLALAAFTHSLRRHLGAMLASL-TRLDALVFAGGIGENYRSLWP 332
                                               ***********************************************.55******************* PP

                                 TIGR00016 348 lvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDa 400
                                                v+e+++ + ++ld+e         ++ ist++s+++v vi+  e++ +++ a
  lcl|FitnessBrowser__SynE:Synpcc7942_2079 333 AVCEHFAGMPIRLDPEAMA---VAGDRRISTPDSAITVWVIHSREDWQMVQLA 382
                                               ****************998...789999*******************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (393 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: 7.67
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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