GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Cupriavidus basilensis 4G11

Align propionate kinase (EC 2.7.2.15) (characterized)
to candidate RR42_RS03800 RR42_RS03800 acetate kinase

Query= BRENDA::O06961
         (402 letters)



>FitnessBrowser__Cup4G11:RR42_RS03800
          Length = 408

 Score =  262 bits (669), Expect = 2e-74
 Identities = 167/405 (41%), Positives = 243/405 (60%), Gaps = 27/405 (6%)

Query: 5   PVVLVINCGSSSIKFSVLDV-----ATCD---VLMA-------GIADGMNTENAFLSING 49
           P +LV+N GSSS+K SV  V     A  D   VL A       G++  ++   A   I  
Sbjct: 6   PTILVVNAGSSSVKVSVYAVPEAAHANADINPVLSAHGQIEGIGVSPRLSASMADGRIVA 65

Query: 50  DKPINLAH-SNYEDALKAIAFELEKRDLTDSVALIGHRIAHGGELFTQSVIITDEIIDNI 108
           D+   +A  ++++ A + I   L           IGHR+ HGG  F+ +V I D++I  +
Sbjct: 66  DERFPVAQVADHDAAFRLIRLVLSIGLRDAPPVAIGHRVVHGGADFSAAVKIDDDVITKL 125

Query: 109 RRVSPLAPLHNYANLSGIDAARHLFPAVRQVAVFDTSFHQTLAPEAYLYGLPWEYFSSLG 168
             + PLAPLH   NL+ I A R   PA+ QVA FDT+FH    P A L  LP+EYF   G
Sbjct: 126 EALIPLAPLHQPHNLTAIRAVRAAVPALLQVACFDTAFHAGHDPLAQLLALPYEYFER-G 184

Query: 169 VRRYGFHGTSHRYVSRRAYELLDLDEKDSGLIVAHLGNGASICAVRNGQSVDTSMGMTPL 228
           +RRYGFHG S+ Y++RR  ++   D     +IVAHLGNGAS+CA+R+G+SV+++MG+T L
Sbjct: 185 IRRYGFHGLSYEYIARRLQQIAP-DLAQGRVIVAHLGNGASLCAMRDGRSVESTMGLTAL 243

Query: 229 EGLMMGTRSGDVDFGAMAWIAKETGQTLSDLERVVNKESGLLGISGLSSDLRVLEKAWHE 288
           +GL MGTR G +D GA+ W++++ G +  D+E ++ +ESGL G+SG+SSD+R L  +   
Sbjct: 244 DGLPMGTRCGAIDAGAILWLSQQ-GMSTKDIETMLYQESGLKGLSGVSSDMRALLAS--- 299

Query: 289 GHERARLAIKTFVHRIARHIAGHAASLHRLDGIIFTGGIGENSVLIRQLVIEHLG-VLGL 347
              RARLAI  + +R A+ I   AA+L  LD ++FT GIG NS  +R+ +   L  + G+
Sbjct: 300 DAPRARLAIDFYAYRAAQEIGKLAATLGGLDALVFTAGIGANSPPVREKICARLADLFGI 359

Query: 348 TLDVEMNKQPNSHGERIISANPSQVICAVIPTNEEKMIALDAIHL 392
           +LD   N   N + +R IS + S+V   V+PT+EE MIAL+   +
Sbjct: 360 SLDAGAN---NENRQR-ISRDNSRVPVLVLPTDEEGMIALNTARI 400


Lambda     K      H
   0.320    0.137    0.397 

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: 396
Number of extensions: 20
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: 402
Length of database: 408
Length adjustment: 31
Effective length of query: 371
Effective length of database: 377
Effective search space:   139867
Effective search space used:   139867
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 RR42_RS03800 RR42_RS03800 (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.11244.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     5e-110  353.9   0.0     6e-110  353.6   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS03800  RR42_RS03800 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS03800  RR42_RS03800 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  353.6   0.0    6e-110    6e-110       4     404 ..       6     401 ..       3     402 .. 0.88

  Alignments for each domain:
  == domain 1  score: 353.6 bits;  conditional E-value: 6e-110
                                 TIGR00016   4 kkilvlnaGssslkfalldaensekv........llsglverikleeariktvedge..kkeee.klai 61 
                                                 ilv+naGsss+k +++   ++ +          ++g +e i ++      + dg     e++ + ++
  lcl|FitnessBrowser__Cup4G11:RR42_RS03800   6 PTILVVNAGSSSVKVSVYAVPEAAHAnadinpvlSAHGQIEGIGVSPRLSASMADGRivADERFpVAQV 74 
                                               679***************988744333444554346789999999988777666665222333314567 PP

                                 TIGR00016  62 edheeavkkllntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpae 130
                                               +dh++a + +   l     i    +   +iGHRvvhGg +f+ +v ++d+v+ k++ +++lAPlH p +
  lcl|FitnessBrowser__Cup4G11:RR42_RS03800  75 ADHDAAFRLIRLVLS----IGLRDAPPVAIGHRVVHGGADFSAAVKIDDDVITKLEALIPLAPLHQPHN 139
                                               777777766655555....6667777789**************************************** PP

                                 TIGR00016 131 legieavlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakl 199
                                               l++i+av     ++   +va+FDtafH      a l alPy++++  g+RrYGfHG+s++y+++r++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS03800 140 LTAIRAVR--AAVPALLQVACFDTAFHAGHDPLAQLLALPYEYFE-RGIRRYGFHGLSYEYIARRLQQI 205
                                               ********..5666667************************9885.7*******************998 PP

                                 TIGR00016 200 lnkplddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglslde 268
                                                   l++ ++iv+HlGnGas++a+++G+s++ +mGlt L+Gl mGtR+G iD ++i +l+ ++g+s+++
  lcl|FitnessBrowser__Cup4G11:RR42_RS03800 206 APD-LAQGRVIVAHLGNGASLCAMRDGRSVESTMGLTALDGLPMGTRCGAIDAGAILWLS-QQGMSTKD 272
                                               766.99****************************************************96.68****** PP

                                 TIGR00016 269 ieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgG 337
                                               ie++l ++sGl g+sg+ssD+R +l+       +a+lA++ y++R a+ igk +a+l g lDa+vFt+G
  lcl|FitnessBrowser__Cup4G11:RR42_RS03800 273 IETMLYQESGLKGLSGVSSDMRALLASD---APRARLAIDFYAYRAAQEIGKLAATLGG-LDALVFTAG 337
                                               ************************9887...679***********************76.********* PP

                                 TIGR00016 338 iGenaaevrelvlekle.vlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDalrla 404
                                               iG n+  vre+++ +l+ ++G+ ld   nn    ++ + is ++s+v vlv+pt+ee +ia +++r++
  lcl|FitnessBrowser__Cup4G11:RR42_RS03800 338 IGANSPPVREKICARLAdLFGISLDAGANN----ENRQRISRDNSRVPVLVLPTDEEGMIALNTARIM 401
                                               **************997367********99....66778**********************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (408 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: 12.11
//
[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