GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SynE:Synpcc7942_2079
          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.1650.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: 7.27
//
[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