GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ackA in Azospirillum brasilense Sp245

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate AZOBR_RS12495 AZOBR_RS12495 acetate kinase

Query= SwissProt::P37877
         (395 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS12495 AZOBR_RS12495 acetate
           kinase
          Length = 402

 Score =  284 bits (726), Expect = 4e-81
 Identities = 168/390 (43%), Positives = 234/390 (60%), Gaps = 15/390 (3%)

Query: 4   IIAINAGSSSLKFQLFEMPSETVLTKGLVERI-GIADSVFTISVNGEKNTEVTDI----- 57
           I+ INAGSSSLKF +F       L   +  +I GI       + +  KN     +     
Sbjct: 12  ILVINAGSSSLKFSVFRESGAGGLRVTINGQISGIGTEPKFEAKDAAKNPLAERVWAAGE 71

Query: 58  PDHAVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISEL 117
           P    A+   L +  E  +  D  ++   GHRVVHGG + +  VLLT   ++E+E    L
Sbjct: 72  PSDRTALLAFLLEWIEGRL--DGAKLLAAGHRVVHGGTRHAAPVLLTPAVMEELESFIPL 129

Query: 118 APLHNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGF 177
           APLH P N+  I+A  E  P +P VA FDTAFH+  P QS ++++P E  ++ G+R+YGF
Sbjct: 130 APLHQPHNLAAIRALAEAHPELPQVACFDTAFHRGQPWQSQMFAIPRELTDE-GVRRYGF 188

Query: 178 HGTSHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMG 237
           HG S++Y+  R  EL    L D R++  HLG+GAS+ A+  G+S+D++MGFT L G+ MG
Sbjct: 189 HGLSYEYIARRLPELAPE-LADGRVVVAHLGSGASMCAIHAGRSVDSTMGFTALDGLPMG 247

Query: 238 TRSGNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAE 297
           TR GNIDP ++ Y+M + G  AD +   L  KSGLLG+SG S+D+R ++++    +  AE
Sbjct: 248 TRCGNIDPGVLIYLMRQKGMGADAIEKLLYNKSGLLGVSGLSNDMRALLDSE---DPHAE 304

Query: 298 TALEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALN 357
            A+E+F  RI K  G+ AA M G+DA++FTAGIGE S  VR RV   L ++GV  DPA N
Sbjct: 305 EAVELFCFRIAKETGALAASMGGIDALVFTAGIGERSAPVRARVGDKLAWLGVILDPAAN 364

Query: 358 NVRGEEAFISYPHSPVKVMIIPTDEEVMIA 387
              G    IS P+S + V +IPTDEE MIA
Sbjct: 365 EANG--PLISAPNSRIPVYVIPTDEEQMIA 392


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: 378
Number of extensions: 28
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: 395
Length of database: 402
Length adjustment: 31
Effective length of query: 364
Effective length of database: 371
Effective search space:   135044
Effective search space used:   135044
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_RS12495 AZOBR_RS12495 (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.27342.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-114  369.0   0.0   1.5e-114  368.8   0.0    1.0  1  lcl|FitnessBrowser__azobra:AZOBR_RS12495  AZOBR_RS12495 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS12495  AZOBR_RS12495 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  368.8   0.0  1.5e-114  1.5e-114       5     399 ..      11     394 ..       8     400 .. 0.90

  Alignments for each domain:
  == domain 1  score: 368.8 bits;  conditional E-value: 1.5e-114
                                 TIGR00016   5 kilvlnaGssslkfalldaen..sekvllsglverikleeariktv.edge..kkeeeklaiedheeav 68 
                                                ilv+naGssslkf+++  ++  + +v ++g +  i  e ++  +   ++   ++  +  + +d+++ +
  lcl|FitnessBrowser__azobra:AZOBR_RS12495  11 AILVINAGSSSLKFSVFRESGagGLRVTINGQISGIGTEPKFEAKDaAKNPlaERVWAAGEPSDRTALL 79 
                                               79***************9998545677899999999988664443313443112333445556677777 PP

                                 TIGR00016  69 kkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieav 137
                                               ++ll+ ++     + + +++ + GHRvvhGg++++  v++t  v+++++ +++lAPlH p +l +i+a+
  lcl|FitnessBrowser__azobra:AZOBR_RS12495  80 AFLLEWIEG----RLDGAKLLAAGHRVVHGGTRHAAPVLLTPAVMEELESFIPLAPLHQPHNLAAIRAL 144
                                               777777775....5678899999********************************************** PP

                                 TIGR00016 138 lklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkpldd 206
                                                  + +++ ++va+FDtafH+  p ++ ++a+P++l ++ gvRrYGfHG+s++y+++r+ +l    l+d
  lcl|FitnessBrowser__azobra:AZOBR_RS12495 145 A--EAHPELPQVACFDTAFHRGQPWQSQMFAIPREL-TDEGVRRYGFHGLSYEYIARRLPELAPE-LAD 209
                                               9..99999*************************776.567*******************997665.9** PP

                                 TIGR00016 207 lnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnk 275
                                                +++v+HlG Gas++a++ G+s+d +mG+t L+Gl mGtR+G+iDp+++ yl+ ++g+ +d+ie++l  
  lcl|FitnessBrowser__azobra:AZOBR_RS12495 210 GRVVVAHLGSGASMCAIHAGRSVDSTMGFTALDGLPMGTRCGNIDPGVLIYLMRQKGMGADAIEKLLYN 278
                                               ********************************************************************* PP

                                 TIGR00016 276 ksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaae 344
                                               ksGllg+sgls+D+R +ld     + +a+ A+++++ Riak  g+ +as+ g +Da+vFt+GiGe +a 
  lcl|FitnessBrowser__azobra:AZOBR_RS12495 279 KSGLLGVSGLSNDMRALLDSE---DPHAEEAVELFCFRIAKETGALAASMGG-IDALVFTAGIGERSAP 343
                                               ******************998...6679**********************76.**************** PP

                                 TIGR00016 345 vrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeD 399
                                               vr++v +kl+ lG+ ld++ n+     +  +is ++s++ v+vipt+ee +ia  
  lcl|FitnessBrowser__azobra:AZOBR_RS12495 344 VRARVGDKLAWLGVILDPAANE----ANGPLISAPNSRIPVYVIPTDEEQMIALH 394
                                               *******************999....7789**********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (402 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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.45
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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