GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Azospirillum thiophilum BV-S

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_045581906.1 AL072_RS00850 acetate/propionate family kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_001305595.1:WP_045581906.1
          Length = 394

 Score =  276 bits (707), Expect = 6e-79
 Identities = 170/392 (43%), Positives = 231/392 (58%), Gaps = 20/392 (5%)

Query: 4   IIAINAGSSSLKFQLFEMPS---ETVLTKGLVERIGIADSVFTISVNGE-----KNTEVT 55
           I+ INAGSSSLKF +F         V   G +  IG    VF            K+ E  
Sbjct: 5   ILVINAGSSSLKFSVFRDHGGGDPVVTLNGQISGIG-TQPVFEAKDAQRRPLAGKSWEAE 63

Query: 56  DIPDHAVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDIS 115
           +  D    +  LL+ + E     D   +   GHRVVHGG + +  VLLT   + E++ + 
Sbjct: 64  ERSDRKALLSYLLDWIEER---LDGATLIAAGHRVVHGGVRHAAPVLLTPAVMDELDGLV 120

Query: 116 ELAPLHNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKY 175
            LAPLH P N+  I+A  E  P +P VA FDTAFH+  P Q+  +++P E  E+ G+R+Y
Sbjct: 121 PLAPLHQPHNLAAIRALAEAHPELPQVACFDTAFHRNQPWQAQTFAIPRELTEE-GVRRY 179

Query: 176 GFHGTSHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVA 235
           GFHG S++Y+  R  E +   L D R++  HLG+GAS+ A+ GG+S+D++MGFT L G+ 
Sbjct: 180 GFHGLSYEYIARRLPE-IAPELGDSRVVVAHLGSGASMCAIHGGRSVDSTMGFTALDGLP 238

Query: 236 MGTRSGNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNER 295
           MGTR G IDP ++ Y+M K G  AD +   L  KSGLLG+SG S+D+R ++E+T   +  
Sbjct: 239 MGTRCGTIDPGVLIYLMRK-GMDADGIEKMLYNKSGLLGVSGISNDMRALLEST---DPH 294

Query: 296 AETALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPA 355
           A+ A+E+F  RI K  G+ AA M GVDA++FTAGIGE S  VR RV   L +MG+  D A
Sbjct: 295 AQEAVELFCFRIAKETGALAASMGGVDALVFTAGIGERSAPVRARVGDKLAWMGMELDDA 354

Query: 356 LNNVRGEEAFISYPHSPVKVMIIPTDEEVMIA 387
            N      A IS P S + V +IPTDEE MIA
Sbjct: 355 ANEANA--AKISTPGSRLPVYVIPTDEERMIA 384


Lambda     K      H
   0.317    0.136    0.381 

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: 360
Number of extensions: 28
Number of successful extensions: 7
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: 395
Length of database: 394
Length adjustment: 31
Effective length of query: 364
Effective length of database: 363
Effective search space:   132132
Effective search space used:   132132
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 WP_045581906.1 AL072_RS00850 (acetate/propionate family 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.1251500.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-112  362.3   0.0   1.6e-112  362.2   0.0    1.0  1  NCBI__GCF_001305595.1:WP_045581906.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001305595.1:WP_045581906.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  362.2   0.0  1.6e-112  1.6e-112       3     403 ..       2     390 ..       1     392 [. 0.88

  Alignments for each domain:
  == domain 1  score: 362.2 bits;  conditional E-value: 1.6e-112
                             TIGR00016   3 skkilvlnaGssslkfalldaensekv..llsglverikleeariktvedgekkeeeklaiedhe.eavkkll 72 
                                           s+ ilv+naGssslkf+++  +++      l+g +  i  +    +  +d++++  + +  e+ e +  k+ll
  NCBI__GCF_001305595.1:WP_045581906.1   2 SNAILVINAGSSSLKFSVFRDHGGGDPvvTLNGQISGIGTQPV--FEAKDAQRRPLAGKSWEAEErSDRKALL 72 
                                           678****************999854431256777777777766..5556665555444444333303345566 PP

                             TIGR00016  73 ntlkkdkkilkel..seialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvl 143
                                           + l +   i + l  + + + GHRvvhGg +++  v++t  v++++  +++lAPlH p +l +i+a+   + +
  NCBI__GCF_001305595.1:WP_045581906.1  73 SYLLD--WIEERLdgATLIAAGHRVVHGGVRHAAPVLLTPAVMDELDGLVPLAPLHQPHNLAAIRALA--EAH 141
                                           66663..45555511566677**********************************************9..999 PP

                             TIGR00016 144 lkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGn 216
                                           ++ ++va+FDtafH+  p +a  +a+P++l +e gvRrYGfHG+s++y+++r+ ++    l d++++v+HlG 
  NCBI__GCF_001305595.1:WP_045581906.1 142 PELPQVACFDTAFHRNQPWQAQTFAIPREL-TEEGVRRYGFHGLSYEYIARRLPEIAPE-LGDSRVVVAHLGS 212
                                           99*************************776.567********************99877.9************ PP

                             TIGR00016 217 GasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDl 289
                                           Gas++a++ G+s+d +mG+t L+Gl mGtR+G iDp+++ yl+  +g+ +d ie++l  ksGllg+sg+s+D+
  NCBI__GCF_001305595.1:WP_045581906.1 213 GASMCAIHGGRSVDSTMGFTALDGLPMGTRCGTIDPGVLIYLMR-KGMDADGIEKMLYNKSGLLGVSGISNDM 284
                                           ******************************************96.69************************** PP

                             TIGR00016 290 RdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldl 362
                                           R +l+ +   + +a+ A+++++ Riak  g+ +as+ g +Da+vFt+GiGe +a vr++v +kl+ +G++ld 
  NCBI__GCF_001305595.1:WP_045581906.1 285 RALLEST---DPHAQEAVELFCFRIAKETGALAASMGG-VDALVFTAGIGERSAPVRARVGDKLAWMGMELDD 353
                                           ****999...6679**********************76.********************************** PP

                             TIGR00016 363 elnnaarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                           + n+     + + ist+ s++ v+vipt+ee +ia  + r+
  NCBI__GCF_001305595.1:WP_045581906.1 354 AANE----ANAAKISTPGSRLPVYVIPTDEERMIALHTRRV 390
                                           9999....67789*********************9887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (394 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.57
//
[ok]

This GapMind analysis is from Sep 24 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