GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS12495
          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.905653.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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 21.52
//
[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