GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Azospirillum brasilense Sp245

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate AZOBR_RS04605 AZOBR_RS04605 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>FitnessBrowser__azobra:AZOBR_RS04605
          Length = 398

 Score =  261 bits (666), Expect = 3e-74
 Identities = 164/405 (40%), Positives = 232/405 (57%), Gaps = 22/405 (5%)

Query: 3   VLVINSGSSSIKYQLIEMEGEK--VLCKGIAERIGIEGSRLVHRVGDEKH-----VIERE 55
           +LVIN+GSSSIK+QL +       V  +G  E IG     +V   G +        +  E
Sbjct: 5   ILVINAGSSSIKFQLFDAADGTLPVRLRGRIEGIGTAPRLIVQESGQDGSRDGGVTLPAE 64

Query: 56  LPDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEV 115
             D        L   +  +LG    +    AVGHRVVHGG  +   V VD+ V+  +E  
Sbjct: 65  SGDGVPGALAFLGAWLRGRLGGAMPV----AVGHRVVHGGPAYDSHVAVDDAVIGTLETY 120

Query: 116 SPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRR 175
            PLAPLH P NL  I+A  KLLP V  VA FDTAFH+   + A  YAIP +   +  +RR
Sbjct: 121 VPLAPLHQPNNLAPIRAIRKLLPDVLQVACFDTAFHRHHSEPADRYAIP-DALHREGVRR 179

Query: 176 YGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGL 235
           YGFHG S+ Y++ R  + L   +   +++  H+G+GAS+ A++ G+ VD++MGFT L+GL
Sbjct: 180 YGFHGLSYEYIAGRLPD-LAPGIAGGRVVVAHLGSGASMCAIQDGRSVDSTMGFTALDGL 238

Query: 236 VMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295
            MGTR G LDP +  ++M+K G+  + +  +L    G+ GLS G S+D+RD+  +    D
Sbjct: 239 PMGTRPGQLDPGVVLYLMDK-GMDARAIERLLYHDCGLKGLS-GISNDVRDLLAST---D 293

Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355
              KL L+ + YR +  IGA AAAM G+D +VFTAG+GE +P  R+ +     +LGV LD
Sbjct: 294 PRAKLALDCFVYRASLAIGALAAAMGGIDGLVFTAGIGERAPAIRKAIAERARWLGVDLD 353

Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400
           +  N          I+TPDSRVK  V+PT+EE MIA  T+ I+ +
Sbjct: 354 EAGNAANAL----CITTPDSRVKGWVIPTDEERMIALHTRAILRR 394


Lambda     K      H
   0.318    0.138    0.391 

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: 401
Number of extensions: 16
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: 403
Length of database: 398
Length adjustment: 31
Effective length of query: 372
Effective length of database: 367
Effective search space:   136524
Effective search space used:   136524
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 AZOBR_RS04605 AZOBR_RS04605 (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.1336778.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   9.7e-102  326.6   0.0     2e-101  325.6   0.0    1.4  1  lcl|FitnessBrowser__azobra:AZOBR_RS04605  AZOBR_RS04605 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS04605  AZOBR_RS04605 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.6   0.0    2e-101    2e-101       4     399 ..       3     387 ..       1     392 [. 0.88

  Alignments for each domain:
  == domain 1  score: 325.6 bits;  conditional E-value: 2e-101
                                 TIGR00016   4 kkilvlnaGssslkfalldaense.kvllsglverikleeariktvedgekkeee..klaiedheeavk 69 
                                               + ilv+naGsss+kf+l+da+++   v l+g +e i  +   i   e+g++++++  ++  ++   +v 
  lcl|FitnessBrowser__azobra:AZOBR_RS04605   3 ETILVINAGSSSIKFQLFDAADGTlPVRLRGRIEGIGTAPRLIV-QESGQDGSRDggVTLPAESGDGVP 70 
                                               689******************965145699******99988555.455554444411222344445666 PP

                                 TIGR00016  70 kllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavl 138
                                                 l  l +  + +   +   ++GHRvvhGg  + + v v+d v+  ++  ++lAPlH p++l  i+a+ 
  lcl|FitnessBrowser__azobra:AZOBR_RS04605  71 GALAFLGAWLRGRLGGAMPVAVGHRVVHGGPAYDSHVAVDDAVIGTLETYVPLAPLHQPNNLAPIRAIR 139
                                               666666653333444455578************************************************ PP

                                 TIGR00016 139 klkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddl 207
                                                 k l+++ +va+FDtafH+   e+a  Ya+P ++ ++ gvRrYGfHG+s++y++ r+ +l    ++  
  lcl|FitnessBrowser__azobra:AZOBR_RS04605 140 --KLLPDVLQVACFDTAFHRHHSEPADRYAIP-DALHREGVRRYGFHGLSYEYIAGRLPDLAP-GIAGG 204
                                               ..8889999***********************.777788******************998655.59*** PP

                                 TIGR00016 208 nlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkk 276
                                               +++v+HlG Gas++a+++G+s+d +mG+t L+Gl mGtR G++Dp+++ yl+++ g+ + +ie++l  +
  lcl|FitnessBrowser__azobra:AZOBR_RS04605 205 RVVVAHLGSGASMCAIQDGRSVDSTMGFTALDGLPMGTRPGQLDPGVVLYLMDK-GMDARAIERLLYHD 272
                                               ***************************************************985.999*********** PP

                                 TIGR00016 277 sGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaev 345
                                                Gl g+sg+s+D+Rd+l+ +   + +aklAl+ +v+R    ig+ +a++ g +D++vFt+GiGe a  +
  lcl|FitnessBrowser__azobra:AZOBR_RS04605 273 CGLKGLSGISNDVRDLLAST---DPRAKLALDCFVYRASLAIGALAAAMGG-IDGLVFTAGIGERAPAI 337
                                               *****************998...789***********************76.***************** PP

                                 TIGR00016 346 relvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeD 399
                                               r+ + e+ + lG++ld++ n      +   i+t++s+vk  vipt+ee +ia  
  lcl|FitnessBrowser__azobra:AZOBR_RS04605 338 RKAIAERARWLGVDLDEAGNA----ANALCITTPDSRVKGWVIPTDEERMIALH 387
                                               ****************99998....67789*********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (398 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: 14.67
//
[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