Alignments for a candidate for ackA in Cupriavidus basilensis 4G11

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.32020.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.08
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources