Alignments for a candidate for ackA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Burkholderia phytofirmans PsJN

Align Probable propionate kinase; EC 2.7.2.15 (characterized)
to candidate BPHYT_RS26200 BPHYT_RS26200 acetate kinase

Query= SwissProt::P74879
         (404 letters)



>FitnessBrowser__BFirm:BPHYT_RS26200
          Length = 386

 Score =  243 bits (621), Expect = 5e-69
 Identities = 157/398 (39%), Positives = 206/398 (51%), Gaps = 28/398 (7%)

Query: 5   IMAINAGSSSLKFQLLEMPQGD--MLCQGLIERIGMADAQVTIKTHSQKW--QETVPVAD 60
           I+ +N+GSSSLKF L      D  +L +G  E IG  D  + IK    +   Q+   +  
Sbjct: 12  ILVLNSGSSSLKFGLFRRAGNDESLLLEGSAEGIGRDDGSLRIKAPDGRVLVQQERVLES 71

Query: 61  HRDAVTLLLEKLLGYQIINSLRDIDGVGHRVAHGGEFFKDSTLVTDETLAQIERLAELAP 120
             DA+  L + L              VGHRV HGG   +    +T +   Q+      AP
Sbjct: 72  QIDALQKLAQVLKEQHHARPA----AVGHRVVHGGPRLRTHQRITADVRRQLHEAVHFAP 127

Query: 121 LHNPVNALGIHVFRQLLPDAPSVAVFDTAFHQTLDEPAYIYPLPWHYYAELGIRRYGFHG 180
           LH P     I    ++  DAP  A FDTAFH TL   A    LP   YAE G+ RYGFHG
Sbjct: 128 LHIPPALALIDEAEKIFDDAPHFACFDTAFHATLPLRAAHLALP-RRYAEAGVMRYGFHG 186

Query: 181 TSHKYVSGVLAEKLGVPLSALRVICCHLGNGSSICAIKNGRSVNTSMGFTPQSGVMMGTR 240
            S++     L  +LG  L A R +  HLGNGSS+CA+++GRS++TSMG TP  GV MGTR
Sbjct: 187 LSYES----LVTRLGADLPA-RAVFAHLGNGSSVCALRDGRSIDTSMGLTPTGGVPMGTR 241

Query: 241 SGDIDPSILPWIAQRESKTPQQLNQLLNNESGLLGVSGVSSDYRDVEQAANTGNRQAKLA 300
           SGD+DP +L ++ + E      L  LLN +SGL G +   SD + +E+ A  G+  A LA
Sbjct: 242 SGDLDPGVLLYLMRVEKLDAGALETLLNRQSGLAGYADGESDMQALEKRAAAGDTNASLA 301

Query: 301 LTLFAERIRATIGSYIMQMGGLDALVFTGGIGENSARARSAVCHNLQFLGLAVDEEKNQR 360
           L  FA  +R TIG Y   +GG+D LVFTGGIGE+S   R  VC  L F+GL   +     
Sbjct: 302 LDAFATAVRKTIGGYAALLGGIDLLVFTGGIGEHSQEIRKRVCDGLAFMGLTQSDPAG-- 359

Query: 361 NATFIQTENALVKVAVINTNEELMIAQDVMRIALPATE 398
                       KV  I+T EE  IA+    +   AT+
Sbjct: 360 ------------KVRAIHTEEEKQIARHCRTLLQQATQ 385


Lambda     K      H
   0.319    0.135    0.392 

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: 371
Number of extensions: 14
Number of successful extensions: 4
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: 404
Length of database: 386
Length adjustment: 31
Effective length of query: 373
Effective length of database: 355
Effective search space:   132415
Effective search space used:   132415
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 BPHYT_RS26200 BPHYT_RS26200 (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.7320.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    4.3e-96  308.0   0.0    1.2e-95  306.5   0.0    1.6  1  lcl|FitnessBrowser__BFirm:BPHYT_RS26200  BPHYT_RS26200 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS26200  BPHYT_RS26200 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.5   0.0   1.2e-95   1.2e-95       3     366 ..       9     361 ..       7     378 .. 0.91

  Alignments for each domain:
  == domain 1  score: 306.5 bits;  conditional E-value: 1.2e-95
                                TIGR00016   3 skkilvlnaGssslkfalldaen.sekvllsglverikleeariktv.edgekkeeeklaiedheeavkk 70 
                                              ++ ilvln+Gssslkf l+  ++  e++ll+g +e i  ++  + ++  dg    +++   e++  a++k
  lcl|FitnessBrowser__BFirm:BPHYT_RS26200   9 DQTILVLNSGSSSLKFGLFRRAGnDESLLLEGSAEGIGRDDGSLRIKaPDGRVLVQQERVLESQIDALQK 78 
                                              578****************9886356779*********999887777356666677778889999***** PP

                                TIGR00016  71 llntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlkl 140
                                              l++ lk+     ++++  a++GHRvvhGg ++     +t++v +++++++++APlH p++l  i+++   
  lcl|FitnessBrowser__BFirm:BPHYT_RS26200  79 LAQVLKE-----QHHARPAAVGHRVVHGGPRLRTHQRITADVRRQLHEAVHFAPLHIPPALALIDEAE-- 141
                                              *****95.....6788999*************************************************.. PP

                                TIGR00016 141 kvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnli 210
                                              k+  +a++ a+FDtafH t+p +a+  alP + y e gv rYGfHG+s++ +  r+   l       + +
  lcl|FitnessBrowser__BFirm:BPHYT_RS26200 142 KIFDDAPHFACFDTAFHATLPLRAAHLALP-RRYAEAGVMRYGFHGLSYESLVTRLGADLPA-----RAV 205
                                              889999************************.67899*************8777666655544.....89* PP

                                TIGR00016 211 vcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGll 280
                                               +HlGnG+sv+a+++G+sidtsmGltP  G+ mGtRsGd+Dp+++ yl+  ++l + ++e++ln++sGl 
  lcl|FitnessBrowser__BFirm:BPHYT_RS26200 206 FAHLGNGSSVCALRDGRSIDTSMGLTPTGGVPMGTRSGDLDPGVLLYLMRVEKLDAGALETLLNRQSGLA 275
                                              ********************************************************************** PP

                                TIGR00016 281 gisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvl 350
                                              g ++  sD+  ++++ ++g+ +a+lAl+ ++  ++k ig y+a l g +D +vFtgGiGe ++e+r++v+
  lcl|FitnessBrowser__BFirm:BPHYT_RS26200 276 GYADGESDMQALEKRAAAGDTNASLALDAFATAVRKTIGGYAALLGG-IDLLVFTGGIGEHSQEIRKRVC 344
                                              *********************************************66.********************** PP

                                TIGR00016 351 eklevlGlkl.dlelnn 366
                                              ++l+++Gl   d++   
  lcl|FitnessBrowser__BFirm:BPHYT_RS26200 345 DGLAFMGLTQsDPAGKV 361
                                              *******9641554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (386 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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.03
# Mc/sec: 4.23
//
[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