GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Rhodobacter ovatus JA234

Align Propionate kinase; EC 2.7.2.15 (characterized)
to candidate WP_035745643.1 CRO07_RS16695 acetate/propionate family kinase

Query= SwissProt::P11868
         (402 letters)



>NCBI__GCF_900207575.1:WP_035745643.1
          Length = 389

 Score =  242 bits (617), Expect = 2e-68
 Identities = 155/391 (39%), Positives = 226/391 (57%), Gaps = 18/391 (4%)

Query: 6   VVLVINCGSSSIK--FSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSYEGA 63
           ++L  N GSS+IK  F  L+A+    L SG+ D  +          G+       +  G 
Sbjct: 5   LILTFNTGSSTIKLGFYALEAAAPRPLASGVIDFRDEPFEVRLTREGKTFSGPITADPGD 64

Query: 64  LKAI---AFELEKRNLNDS-VALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHN 119
           L A+   AF     + N S +A+IGHR+ HGG +FT  A ITD+VI  I  ++ LAPLH 
Sbjct: 65  LTAVLNQAFAWLAGHFNLSRLAVIGHRVVHGGDVFTGPARITDQVIAQIDALARLAPLHQ 124

Query: 120 YANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSH 179
             +L+ I + + L+P V Q A FDT+FH T  P    + LP   Y++ G++RYGFHG S+
Sbjct: 125 PQSLALIRAMRGLYPDVPQTASFDTAFHATNPPLIRRFALPRALYDQ-GIKRYGFHGLSY 183

Query: 180 RYVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGD 239
           RY++ +   L      D+ +V AHLG+GAS+CA+R G+S+D+SMG + L+G+ M TRSG 
Sbjct: 184 RYIAGQLGDLAT----DAKVVAAHLGSGASLCAIRGGKSIDSSMGFSTLDGIPMATRSGA 239

Query: 240 VDFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKT 299
           +D G +  +  +  QSL  +E ++ +ESGLLG+SG  +D R L  +       A  AI  
Sbjct: 240 LDPGVILHLMGEMGQSLKQVETMLYRESGLLGVSGFEADSRELMAS---TRPEAAEAIDL 296

Query: 300 FVHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNS 359
           F  RIA  +A  A S+  +D ++FT GIGE+   IR  V   LA LG E+D +    +N 
Sbjct: 297 FCLRIAGEVARLATSMGGIDALVFTAGIGEHQPGIRARVAARLAWLGAELDPD----ANE 352

Query: 360 CGERIVSSENARVICAVIPTNEEKMIALDAI 390
            G R +S+  +RV   VIPT+EE +IA +A+
Sbjct: 353 AGSRRISTAASRVQLLVIPTDEESIIAQEAV 383


Lambda     K      H
   0.318    0.134    0.386 

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: 346
Number of extensions: 13
Number of successful extensions: 5
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: 389
Length adjustment: 31
Effective length of query: 371
Effective length of database: 358
Effective search space:   132818
Effective search space used:   132818
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_035745643.1 CRO07_RS16695 (acetate/propionate family 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.1343611.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-100  322.3   0.0   2.4e-100  322.0   0.0    1.0  1  NCBI__GCF_900207575.1:WP_035745643.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900207575.1:WP_035745643.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.0   0.0  2.4e-100  2.4e-100       3     401 ..       3     383 ..       1     386 [. 0.89

  Alignments for each domain:
  == domain 1  score: 322.0 bits;  conditional E-value: 2.4e-100
                             TIGR00016   3 skkilvlnaGssslkfalldaen.sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 
                                             +il  n+Gss +k   +  e  + + l+sg+++    +      v  + +++++   i++    ++++ln+
  NCBI__GCF_900207575.1:WP_035745643.1   3 RDLILTFNTGSSTIKLGFYALEAaAPRPLASGVIDFRDEPFE----VRLTREGKTFSGPITADPGDLTAVLNQ 71 
                                           6789***********99998886244559*****96554444....333334445555555555555555555 PP

                             TIGR00016  75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147
                                             +  + + +ls +a+iGHRvvhGg+ ft  + +td+v+++i  +++lAPlH p+ l  i+a+      ++++
  NCBI__GCF_900207575.1:WP_035745643.1  72 AFAWLAGHFNLSRLAVIGHRVVHGGDVFTGPARITDQVIAQIDALARLAPLHQPQSLALIRAMR--GLYPDVP 142
                                           55544457899*****************************************************..889999* PP

                             TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220
                                           + a FDtafH t p     +alP+ ly+ +g++rYGfHG+s++y++ +    l+  + d +++ +HlG Gas+
  NCBI__GCF_900207575.1:WP_035745643.1 143 QTASFDTAFHATNPPLIRRFALPRALYD-QGIKRYGFHGLSYRYIAGQ----LGDLATDAKVVAAHLGSGASL 210
                                           ***********************88885.7***************876....5666789************** PP

                             TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293
                                           +a++ Gksid smG+  L+G+ m tRsG +Dp++i +l+ + g+sl+++e++l ++sGllg+sg+ +D R+++
  NCBI__GCF_900207575.1:WP_035745643.1 211 CAIRGGKSIDSSMGFSTLDGIPMATRSGALDPGVILHLMGEMGQSLKQVETMLYRESGLLGVSGFEADSRELM 283
                                           ************************************************************************9 PP

                             TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366
                                           + +   + ea+ A+++++ Ria  +++ ++s+ g +Da+vFt+GiGe +  +r++v  +l+ lG +ld++ n+
  NCBI__GCF_900207575.1:WP_035745643.1 284 AST---RPEAAEAIDLFCLRIAGEVARLATSMGG-IDALVFTAGIGEHQPGIRARVAARLAWLGAELDPDANE 352
                                           988...77899*********************76.*************************************9 PP

                             TIGR00016 367 aarsgkesvisteeskvkvlviptneelviaeDal 401
                                                 ++ ist  s+v++lvipt+ee++ia++a+
  NCBI__GCF_900207575.1:WP_035745643.1 353 ----AGSRRISTAASRVQLLVIPTDEESIIAQEAV 383
                                           ....78899***********************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (389 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 20.29
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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