GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Paraburkholderia bryophila 376MFSha3.1

Align acetate kinase monomer (EC 2.7.2.15) (characterized)
to candidate H281DRAFT_01409 H281DRAFT_01409 acetate kinase

Query= metacyc::ACKCLOS-MONOMER
         (401 letters)



>FitnessBrowser__Burk376:H281DRAFT_01409
          Length = 393

 Score =  253 bits (645), Expect = 9e-72
 Identities = 151/401 (37%), Positives = 224/401 (55%), Gaps = 20/401 (4%)

Query: 4   LVINCGSSSIKYQFIDMKDETV--LAKGLVERIGIKGSVITHKVNGEKYVTETPME---- 57
           LV+N GSSSIK+   D +   +  + +G ++ +            G +       +    
Sbjct: 6   LVLNAGSSSIKFSAFDAQTAELACVLRGQIDGLFSSPHFAAFDAAGAQAGAHAWGDGASL 65

Query: 58  DHKKAIKLVLDALLNDEYGVIKNIDEISAVGHRIVHGGEKYANSVLIDEDVMKSIEDCVS 117
           DH +AI  + D L     G       ++AVGHR+VHGG ++   VL+D  V+  +     
Sbjct: 66  DHAEAIAHIADFLRGHREG-----HRLTAVGHRVVHGGARFVAPVLVDASVLAELHTLTP 120

Query: 118 LAPLHNPPHIIGINACKELMPNVPMVAVFDTAFHQTIPDYAYMYAIPYEYYDKYKIRKYG 177
           LAPLH P ++  I    E    +P +A FDTAFH T P+ A  +A+P    ++  +R+YG
Sbjct: 121 LAPLHQPHNLKPIAIIAERNSAMPQIACFDTAFHATQPEQAKAFALPAAVTER-GVRRYG 179

Query: 178 FHGTSHKYVSRTAAEFIGKKVEDLKMVVCHMGNGASITAVENGKSVDTSMGFTPLGGLAM 237
           FHG S++Y++    E         + VV H+GNGAS+ A+   +SV T+MGFT L GL M
Sbjct: 180 FHGLSYEYIASRLPEMSPAAAAG-RTVVAHLGNGASLCALSACRSVATTMGFTALDGLMM 238

Query: 238 GTRSGDMDPAVVTFLMDKLNINASEVNNLLNKKSGIEGLSGISSDMRDIKKGNYVDKDPK 297
           GTRSG +DP V+ +L+++LN+   EV NLL  +SG+ G+SGIS DMR +        DP+
Sbjct: 239 GTRSGSLDPGVILYLLNELNMTTREVENLLYSQSGLLGVSGISGDMRVL----LASDDPR 294

Query: 298 AMLAYSVFNYKIKQFIGSYTAVMNGLDCLVFTGGIGENSFENRREICKNMDYLGIKIDDK 357
           A  A  ++ Y+I + +GS  A + G+D LVFT GIGE++ + R+ I +   + GI ID  
Sbjct: 295 ARFAVELYVYRICRELGSLIAALKGIDALVFTAGIGEHATQVRQRIGEYAQWCGIDIDSD 354

Query: 358 KNDETMGIPMDISAEGSKVRVLVIPTNEELMIARDTKDIVG 398
            N         IS   S+V V ++PTNEELMIAR T+ ++G
Sbjct: 355 ANQANDSC---ISTPTSRVGVWIVPTNEELMIARHTRALIG 392


Lambda     K      H
   0.317    0.136    0.390 

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: 352
Number of extensions: 24
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate H281DRAFT_01409 H281DRAFT_01409 (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.10480.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.1e-118  382.4   0.0   1.2e-118  382.3   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01409  H281DRAFT_01409 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01409  H281DRAFT_01409 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.3   0.0  1.2e-118  1.2e-118       4     402 ..       3     389 ..       1     392 [. 0.92

  Alignments for each domain:
  == domain 1  score: 382.3 bits;  conditional E-value: 1.2e-118
                                    TIGR00016   4 kkilvlnaGssslkfalldaensekv.llsglverikleeariktv.edgekkeee..klaiedhe 65 
                                                   +ilvlnaGsss+kf+ +da+++e   +l+g ++ ++++  +       ++ + ++    a  dh+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01409   3 DVILVLNAGSSSIKFSAFDAQTAELAcVLRGQIDGLFSSPHFAAFDaAGAQAGAHAwgDGASLDHA 68 
                                                  689******************988655899***9988776655444143444444411456779** PP

                                    TIGR00016  66 eavkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpael 131
                                                  ea++++++ l      ++e + ++++GHRvvhGg +f   v+v+++vl++++ +++lAPlH p +l
  lcl|FitnessBrowser__Burk376:H281DRAFT_01409  69 EAIAHIADFLRG----HREGHRLTAVGHRVVHGGARFVAPVLVDASVLAELHTLTPLAPLHQPHNL 130
                                                  ***********7....78999********************************************* PP

                                    TIGR00016 132 egieavlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraa 197
                                                  + i ++   +     +++a+FDtafH t pe+a  +alP  + +e gvRrYGfHG+s++y++ r+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_01409 131 KPIAIIA--ERNSAMPQIACFDTAFHATQPEQAKAFALP-AAVTERGVRRYGFHGLSYEYIASRLP 193
                                                  *****99..8888999***********************.78899********************9 PP

                                    TIGR00016 198 kllnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlg 263
                                                  ++    ++  + +v+HlGnGas++a+   +s+ t+mG+t L+Gl+mGtRsG++Dp++i yl ++l+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01409 194 EMSPA-AAAGRTVVAHLGNGASLCALSACRSVATTMGFTALDGLMMGTRSGSLDPGVILYLLNELN 258
                                                  98766.788899****************************************************** PP

                                    TIGR00016 264 lsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegel 329
                                                  +++ e+e++l  +sGllg+sg+s D+R++l+     + +a+ A+++yv+Ri + +g+ ia+l+g +
  lcl|FitnessBrowser__Burk376:H281DRAFT_01409 259 MTTREVENLLYSQSGLLGVSGISGDMRVLLASD---DPRARFAVELYVYRICRELGSLIAALKG-I 320
                                                  *****************************9887...789***********************88.* PP

                                    TIGR00016 330 DaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelv 395
                                                  Da+vFt+GiGe a++vr+++ e  +  G+++d++ n+     ++s ist+ s+v v ++ptneel+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01409 321 DALVFTAGIGEHATQVRQRIGEYAQWCGIDIDSDANQ----ANDSCISTPTSRVGVWIVPTNEELM 382
                                                  **********************************999....899********************** PP

                                    TIGR00016 396 iaeDalr 402
                                                  ia+ +  
  lcl|FitnessBrowser__Burk376:H281DRAFT_01409 383 IARHTRA 389
                                                  **98765 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.44
//
[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