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

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.1199.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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.29
//
[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