Alignments for a candidate for ackA in Rhizobium johnstonii 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Rhizobium johnstonii 3841

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate WP_011653335.1 RL_RS20135 acetate/propionate family kinase

Query= curated2:B8EIS2
         (404 letters)



>NCBI__GCF_000009265.1:WP_011653335.1
          Length = 392

 Score =  299 bits (765), Expect = 1e-85
 Identities = 171/394 (43%), Positives = 236/394 (59%), Gaps = 11/394 (2%)

Query: 5   VITLNAGSSSIKFALFREGLTQEGSAKELTPMAIGLAEMVGEERRITVHDGAGAKIYEVK 64
           ++T NAGSS++K  +F      EG+  E T +  G+ +   E   +++  G   +I E+ 
Sbjct: 7   LLTFNAGSSTVKIGIF----ATEGT--EATRIGKGVIDFRAEPLSLSLTKGP--QIIEMP 58

Query: 65  RTEHVDAPFHAEALRRILAWRQSAFPDAEVVAAGHRVVHGGVHYSAPVIVTDEVLKYLHT 124
               V    H   +   LA     F      AAGHRVVHGG  ++  + +       +  
Sbjct: 59  LKAEVTEDLHG-VIDETLALLADHFDMTATRAAGHRVVHGGDRFTRAIALDAAATDAVDA 117

Query: 125 LIPLAPLHEPYNIAGILGAREAWPHVEQVACFDTAFHRTHPFVNDVFALPRRFYDEGVRR 184
           L PLAPLH+P  +  I   +   PH+ Q A FDTAFH T   +   FA+PR  +DEG++R
Sbjct: 118 LTPLAPLHQPQALRFIRALKHLKPHLVQTASFDTAFHATQDDLIRRFAIPRALHDEGIKR 177

Query: 185 YGFHGLSYEYIVRRLREIAPLHAAGRVVVAHLGNGASMCAIRDGLSVASSMGFTALDGLP 244
           YGFHGLSY++I   LR  AP HAA +VVVAHLG+GAS+CA+ +G+S   SMGF+ LDG+P
Sbjct: 178 YGFHGLSYKFIAGELRRKAP-HAA-KVVVAHLGSGASLCALDEGVSRDCSMGFSTLDGIP 235

Query: 245 MGTRCGQLDPGVVLYLMQEKKMSAAEITDLLYRESGLKGLSGLSHDMRELEAADTLEAQQ 304
           M TR G LDPGV+L+L  ++K S  EI DLLY  SGL G+SG+S D R+L   D  +A+Q
Sbjct: 236 MATRTGWLDPGVILHLADQRKQSFEEIEDLLYHRSGLLGVSGISADTRDLLKDDRPQARQ 295

Query: 305 AIEYFVFRIRRELGGLAAVLKGIDAIVFCGGIGENSRHVRERVLEGMEWIGVELDRSANS 364
           AI+ F  RI  E+G +AA L G+D +VF  GIGE+   +R  V +   W+G+ +D  AN+
Sbjct: 296 AIDLFTLRIAGEIGRMAATLNGLDTLVFTAGIGEHQSEIRAGVAKRSSWLGLAIDEKANA 355

Query: 365 ANAEVISSERSRTRVFVIPTDEEGMIARHTLALL 398
           AN   IS+ +SR    VI TDEE +IA   L++L
Sbjct: 356 ANDFTISTRKSRIAAHVIATDEEQVIADEALSIL 389


Lambda     K      H
   0.322    0.137    0.404 

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: 387
Number of extensions: 14
Number of successful extensions: 3
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: 404
Length of database: 392
Length adjustment: 31
Effective length of query: 373
Effective length of database: 361
Effective search space:   134653
Effective search space used:   134653
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_011653335.1 RL_RS20135 (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.1765512.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-95  306.5   0.0    1.4e-95  306.3   0.0    1.0  1  NCBI__GCF_000009265.1:WP_011653335.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000009265.1:WP_011653335.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  306.3   0.0   1.4e-95   1.4e-95       4     402 ..       5     387 ..       2     390 .. 0.89

  Alignments for each domain:
  == domain 1  score: 306.3 bits;  conditional E-value: 1.4e-95
                             TIGR00016   4 kkilvlnaGssslkfalldaensekv.llsglverikleeariktvedgekkeeekla...iedheeavkkll 72 
                                            ++l  naGss +k  ++ +e++e + + +g+++    + +    +++g +  e  l+   +ed +  +++ l
  NCBI__GCF_000009265.1:WP_011653335.1   5 DLLLTFNAGSSTVKIGIFATEGTEATrIGKGVIDFRAEPLS--LSLTKGPQIIEMPLKaevTEDLHGVIDETL 75 
                                           57899****************98766699****97766666..556666665555544111345555555555 PP

                             TIGR00016  73 ntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllk 145
                                             l +    + ++   ++ GHRvvhGg++ft ++ +++ + +++  +++lAPlH p++l  i+a+++lk++l 
  NCBI__GCF_000009265.1:WP_011653335.1  76 ALLAD----HFDMTATRAAGHRVVHGGDRFTRAIALDAAATDAVDALTPLAPLHQPQALRFIRALKHLKPHLV 144
                                           55554....3466677899***********************************************7766665 PP

                             TIGR00016 146 aknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGa 218
                                             + a FDtafH t  +    +a+P ++ ++ g++rYGfHG+s+k+++ ++ ++   + +  +++v+HlG Ga
  NCBI__GCF_000009265.1:WP_011653335.1 145 --QTASFDTAFHATQDDLIRRFAIP-RALHDEGIKRYGFHGLSYKFIAGELRRK---APHAAKVVVAHLGSGA 211
                                           ..9**********************.566788***************9988875...555899********** PP

                             TIGR00016 219 svsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRd 291
                                           s++a+ +G s d smG+  L+G+ m tR+G +Dp++i +la+++++s +eie++l  +sGllg+sg+s+D Rd
  NCBI__GCF_000009265.1:WP_011653335.1 212 SLCALDEGVSRDCSMGFSTLDGIPMATRTGWLDPGVILHLADQRKQSFEEIEDLLYHRSGLLGVSGISADTRD 284
                                           ************************************************************************* PP

                             TIGR00016 292 ildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlel 364
                                           +l++    + +a+ A+++++ Ria  ig+++a+l+g lD++vFt+GiGe ++e+r+ v ++   lGl++d++ 
  NCBI__GCF_000009265.1:WP_011653335.1 285 LLKDD---RPQARQAIDLFTLRIAGEIGRMAATLNG-LDTLVFTAGIGEHQSEIRAGVAKRSSWLGLAIDEKA 353
                                           *9877...889***********************88.**********************************99 PP

                             TIGR00016 365 nnaarsgkesvisteeskvkvlviptneelviaeDalr 402
                                           n      ++  ist++s++ + vi t+ee via +al 
  NCBI__GCF_000009265.1:WP_011653335.1 354 NA----ANDFTISTRKSRIAAHVIATDEEQVIADEALS 387
                                           99....8899***********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (392 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 27.37
//
[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