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.4033.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: 0.06u 0.01s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 2.45
//
[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