Alignments for a candidate for ackA in Methylotuvimicrobium alcaliphilum 20Z

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Methylotuvimicrobium alcaliphilum 20Z

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_014149283.1 MEALZ_RS13880 acetate kinase

Query= BRENDA::G4T0C7
         (401 letters)



>NCBI__GCF_000968535.2:WP_014149283.1
          Length = 401

 Score =  797 bits (2059), Expect = 0.0
 Identities = 401/401 (100%), Positives = 401/401 (100%)

Query: 1   MTIPNGNILVINSGSSSIKYRLIALPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIK 60
           MTIPNGNILVINSGSSSIKYRLIALPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIK
Sbjct: 1   MTIPNGNILVINSGSSSIKYRLIALPQEQVLADGLLERIGEQESRIIHRADDSGRLNEIK 60

Query: 61  QSVIAADHHQAFKAVFEILGENCSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRIA 120
           QSVIAADHHQAFKAVFEILGENCSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRIA
Sbjct: 61  QSVIAADHHQAFKAVFEILGENCSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRIA 120

Query: 121 PLHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGFH 180
           PLHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGFH
Sbjct: 121 PLHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGFH 180

Query: 181 GTSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMGT 240
           GTSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMGT
Sbjct: 181 GTSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLEGLVMGT 240

Query: 241 RSGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTNDLRTVLEQTNAGDERARLA 300
           RSGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTNDLRTVLEQTNAGDERARLA
Sbjct: 241 RSGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTNDLRTVLEQTNAGDERARLA 300

Query: 301 LDLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAANSD 360
           LDLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAANSD
Sbjct: 301 LDLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAANSD 360

Query: 361 VTGAIAEIGLAESRTRILVIKTDEELQIAREAMAVLDKDHA 401
           VTGAIAEIGLAESRTRILVIKTDEELQIAREAMAVLDKDHA
Sbjct: 361 VTGAIAEIGLAESRTRILVIKTDEELQIAREAMAVLDKDHA 401


Lambda     K      H
   0.320    0.137    0.400 

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: 721
Number of extensions: 9
Number of successful extensions: 1
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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 WP_014149283.1 MEALZ_RS13880 (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.824592.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-144  468.0   0.0   1.4e-144  467.7   0.0    1.0  1  NCBI__GCF_000968535.2:WP_014149283.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000968535.2:WP_014149283.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.7   0.0  1.4e-144  1.4e-144       5     403 ..       7     395 ..       4     397 .. 0.95

  Alignments for each domain:
  == domain 1  score: 467.7 bits;  conditional E-value: 1.4e-144
                             TIGR00016   5 kilvlnaGssslkfalldaensekvllsglverikleeariktvedgekk.e..eeklaiedheeavkkllnt 74 
                                            ilv+n+Gsss+k+ l+     e+vl++gl eri  +e+ri    d++ + +  ++ +  +dh++a k++++ 
  NCBI__GCF_000968535.2:WP_014149283.1   7 NILVINSGSSSIKYRLIALP-QEQVLADGLLERIGEQESRIIHRADDSGRlNeiKQSVIAADHHQAFKAVFEI 78 
                                           69******************.5*****************99887655443130133445689*****999998 PP

                             TIGR00016  75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147
                                           l        e+ ++++iGHRvvhGg++f+  ++v+d+++++++ + ++APlHnp +l gie+ l     + ++
  NCBI__GCF_000968535.2:WP_014149283.1  79 LG-------ENCSVDAIGHRVVHGGDRFSGPALVDDDTIASMRALCRIAPLHNPVNLLGIESCL--AHFPGVP 142
                                           88.......5789***************************************************..7778899 PP

                             TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220
                                           +vavFDtafHqt+p +ay Ya+P+ +y ++g+Rr+GfHGtsh+yv++raa+ ++kp d ++li++HlGnGas 
  NCBI__GCF_000968535.2:WP_014149283.1 143 QVAVFDTAFHQTMPPHAYRYAIPETWYSDYGIRRFGFHGTSHHYVARRAAEFIGKPFDRSHLITLHLGNGASA 215
                                           ************************************************************************* PP

                             TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293
                                           +a+ nG+s+dtsmG+tPLeGlvmGtRsGd+Dpai  ++++t+++ +d+i ++ln++sGl g+ g ++DlR++l
  NCBI__GCF_000968535.2:WP_014149283.1 216 TAIANGRSVDTSMGFTPLEGLVMGTRSGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCG-TNDLRTVL 287
                                           ****************************************************************.******** PP

                             TIGR00016 294 dkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnn 366
                                           +++++g+e+a+lAl++y++Ri+kyig+y a l ge+Da+vFtgG+Genaaevr+l++e+l  lG+++d++ n 
  NCBI__GCF_000968535.2:WP_014149283.1 288 EQTNAGDERARLALDLYCYRIKKYIGAYYAVL-GEVDALVFTGGVGENAAEVRRLACEGLSRLGIAIDEAANS 359
                                           ********************************.66************************************99 PP

                             TIGR00016 367 aarsgkesvisteeskvkvlviptneelviaeDalrl 403
                                              +g  + i   es++++lvi+t+eel ia++a+ +
  NCBI__GCF_000968535.2:WP_014149283.1 360 -DVTGAIAEIGLAESRTRILVIKTDEELQIAREAMAV 395
                                           .8899999************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (401 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: 00:00:00.00
# Mc/sec: 21.66
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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