Alignments for a candidate for ackA in Saccharomonospora marina XMU15

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Saccharomonospora marina XMU15

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_009154259.1 SACMADRAFT_RS12875 acetate/propionate family kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000244955.1:WP_009154259.1
          Length = 375

 Score =  241 bits (616), Expect = 2e-68
 Identities = 131/323 (40%), Positives = 197/323 (60%), Gaps = 2/323 (0%)

Query: 76  GVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLAPLHNPANLMGIKAAMK 135
           G+ +    IDAV  R+VHGG R  E V++ E  L  +EE++P A LH P +L   + AM 
Sbjct: 39  GLAEFAAAIDAVAVRIVHGGNR-AEPVVLTERALAELEELTPYAALHQPRSLAIARHAMA 97

Query: 136 LLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFHGTSHRYVSKRAAEILG 195
            LP VP V  FDTAFH  +P +A  YA+P  +  ++ IRRYGFHG S  Y +   A +LG
Sbjct: 98  ALPRVPVVGCFDTAFHADLPARASTYAVPAAWRREHGIRRYGFHGLSVAYATAWTARLLG 157

Query: 196 KKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGTRSGDLDPAIPFFIMEK 255
           + + +L ++ CH+G G SV AV+ G+ VDTSMG TPL+G+ M TRSG +DPAIP +++ +
Sbjct: 158 RPVAQLGMVCCHLGAGVSVTAVEGGRSVDTSMGLTPLDGVPMATRSGAIDPAIPLYLVRR 217

Query: 256 EGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCKLVLEIYDYRIAKYIGA 315
            G+SP ++   L ++SG+ GLS G S D+RD+  A   GD   +L +E+Y +R+ + I A
Sbjct: 218 AGMSPADVERALQQESGLAGLS-GTSGDIRDVLAARALGDPDARLAVEVYLHRLRREIAA 276

Query: 316 YAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKNEETIRGKEGIISTPDS 375
              +++ VDA+V T GV E+ P    ++ +           ++      G EG+IS PD+
Sbjct: 277 AVVSLSHVDAVVLTGGVAEHQPDLMAELVAGAGLGLSHASARRAAAGGDGAEGVISPPDA 336

Query: 376 RVKVLVVPTNEELMIARDTKEIV 398
            V V+VV + E+L +A  T+ ++
Sbjct: 337 PVPVVVVTSREDLELASQTEHLL 359


Lambda     K      H
   0.318    0.138    0.391 

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: 317
Number of extensions: 13
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 403
Length of database: 375
Length adjustment: 30
Effective length of query: 373
Effective length of database: 345
Effective search space:   128685
Effective search space used:   128685
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_009154259.1 SACMADRAFT_RS12875 (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.1819510.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.5e-95  306.2   0.0    3.3e-93  298.5   0.0    2.0  2  NCBI__GCF_000244955.1:WP_009154259.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000244955.1:WP_009154259.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0   0.00024   0.00024       4      25 ..       1      22 [.       1      32 [. 0.80
   2 !  298.5   0.0   3.3e-93   3.3e-93      84     403 ..      43     358 ..      35     360 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00024
                             TIGR00016  4 kkilvlnaGssslkfalldaen 25
                                          +++l ln Gssslk al+    
  NCBI__GCF_000244955.1:WP_009154259.1  1 MRVLTLNPGSSSLKLALVRDGA 22
                                          579*************987664 PP

  == domain 2  score: 298.5 bits;  conditional E-value: 3.3e-93
                             TIGR00016  84 elseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtaf 156
                                             + i+++  R+vhGg++ +e v++t+ +l+++++++++A lH p  l   ++++    l++++ v +FDtaf
  NCBI__GCF_000244955.1:WP_009154259.1  43 FAAAIDAVAVRIVHGGNR-AEPVVLTERALAELEELTPYAALHQPRSLAIARHAM--AALPRVPVVGCFDTAF 112
                                           56789***********97.789**************************9999999..89999*********** PP

                             TIGR00016 157 HqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksi 229
                                           H  +p +a  Ya+P  + +e+g+RrYGfHG+s  y t  +a+ll++p+++l ++ cHlG G sv+av+ G+s+
  NCBI__GCF_000244955.1:WP_009154259.1 113 HADLPARASTYAVPAAWRREHGIRRYGFHGLSVAYATAWTARLLGRPVAQLGMVCCHLGAGVSVTAVEGGRSV 185
                                           ************************************************************************* PP

                             TIGR00016 230 dtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegnee 302
                                           dtsmGltPL+G+ m tRsG iDpai  yl  + g+s +++e++l+++sGl g+sg s D+Rd+l++ + g+ +
  NCBI__GCF_000244955.1:WP_009154259.1 186 DTSMGLTPLDGVPMATRSGAIDPAIPLYLVRRAGMSPADVERALQQESGLAGLSGTSGDIRDVLAARALGDPD 258
                                           ************************************************************************* PP

                             TIGR00016 303 aklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa.rsgkes 374
                                           a+lA++vy hR+++ i++ + sl++ +Da+v tgG+ e + ++ ++++ + + lGl   +++  aa   g e+
  NCBI__GCF_000244955.1:WP_009154259.1 259 ARLAVEVYLHRLRREIAAAVVSLSH-VDAVVLTGGVAEHQPDLMAELVAG-AGLGLSHASARRAAAgGDGAEG 329
                                           ***********************77.***************999988876.57999999988887768999** PP

                             TIGR00016 375 visteeskvkvlviptneelviaeDalrl 403
                                           vis +++ v v+v+   e+l +a  + +l
  NCBI__GCF_000244955.1:WP_009154259.1 330 VISPPDAPVPVVVVTSREDLELASQTEHL 358
                                           ********************999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (375 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 6.25
//
[ok]

This GapMind analysis is from Sep 24 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