Alignments for a candidate for ackA in Steroidobacter denitrificans DSM 18526

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Steroidobacter denitrificans DSM 18526

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_066921191.1 ACG33_RS11040 acetate/propionate family kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_001579945.1:WP_066921191.1
          Length = 611

 Score =  319 bits (817), Expect = 2e-91
 Identities = 176/409 (43%), Positives = 251/409 (61%), Gaps = 19/409 (4%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKV------LCKGIAERIGIEGSRLVHRVGDEKHVIER 54
           M VL +N GSSS+K  LIE+E   V      +     E +G    R+        H  + 
Sbjct: 1   MLVLALNCGSSSVKMALIEVEPRSVGAHARRMFDARVEGMGGASCRV--------HTRDG 52

Query: 55  ELPDHEE-ALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIE 113
           E+ + E  +L+  ++ L+++  G  +    + AV HRVVHGG       L+DE  L  ++
Sbjct: 53  EIRECEGLSLRAAVSELLEQAGGRARIRDTVQAVAHRVVHGGGELVRPTLIDETSLSTLD 112

Query: 114 EVSPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKI 173
            ++ LAPLHNP     I+   +LLP +P+VAVFDTAFH T+P +A  YA+P E  E++ I
Sbjct: 113 SIAALAPLHNPPAAAAIRICRELLPELPHVAVFDTAFHATLPPRAREYALPREVTERFGI 172

Query: 174 RRYGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLE 233
           RRYGFHGTSH +V   A   +    +EL+II+CH+GNGASVAA++YG+ V+TSMG TPLE
Sbjct: 173 RRYGFHGTSHAHVLSAACVHMNATPQELRIISCHLGNGASVAAIEYGRSVETSMGMTPLE 232

Query: 234 GLVMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALK 293
           GLVMGTR GD+DP +   +++  G     + ++LN ++G+ GL+   ++DMR+IE  A +
Sbjct: 233 GLVMGTRCGDIDPGVLLHLLQSAGFDASALDELLNSRAGLTGLTG--TNDMREIERRAAR 290

Query: 294 GDEWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVK 353
           GDE C+L + +Y +RI KYIGAYAA M GV+ I FT GVGENS + R      L+FLG  
Sbjct: 291 GDEHCRLAITLYAHRIRKYIGAYAAVMGGVEVIAFTGGVGENSALVRHRCMQRLDFLGAV 350

Query: 354 LDKQKNEETIRGKEGI--ISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400
           LD+  N +    + G+  IS   SR ++LVV  +EE  IA D  E++ +
Sbjct: 351 LDEDANRDAGFDEFGVACISEEYSRTRLLVVRADEESAIAGDAAELLAR 399


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: 574
Number of extensions: 23
Number of successful extensions: 4
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: 403
Length of database: 611
Length adjustment: 34
Effective length of query: 369
Effective length of database: 577
Effective search space:   212913
Effective search space used:   212913
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: 52 (24.6 bits)

Align candidate WP_066921191.1 ACG33_RS11040 (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.1680456.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-120  386.7   0.0   8.2e-120  386.1   0.0    1.2  1  NCBI__GCF_001579945.1:WP_066921191.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001579945.1:WP_066921191.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  386.1   0.0  8.2e-120  8.2e-120       4     403 ..       1     396 [.       1     398 [. 0.92

  Alignments for each domain:
  == domain 1  score: 386.1 bits;  conditional E-value: 8.2e-120
                             TIGR00016   4 kkilvlnaGssslkfalldaensekv......llsglverikleeariktvedgekkeeeklaiedheeavkk 70 
                                           +++l ln+Gsss+k+al++ e  ++v      ++++ ve +  +       +++ ++e  + +  + ++av++
  NCBI__GCF_001579945.1:WP_066921191.1   1 MLVLALNCGSSSVKMALIEVEP-RSVgaharrMFDARVEGMGGASC----RVHTRDGEIRECEGLSLRAAVSE 68 
                                           579****************995.44433223345555555554444....34455667788888899999999 PP

                             TIGR00016  71 llntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvl 143
                                           ll++        +  + ++++ HRvvhGg ++   +++++ +l+ +  i+ lAPlHnp+++ +i++    + l
  NCBI__GCF_001579945.1:WP_066921191.1  69 LLEQAGGR---ARIRDTVQAVAHRVVHGGGELVRPTLIDETSLSTLDSIAALAPLHNPPAAAAIRICR--ELL 136
                                           99998864...45678899*************************************************..889 PP

                             TIGR00016 144 lkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGn 216
                                           ++ ++vavFDtafH t+p +a +YalP+++ +++g+RrYGfHGtsh +v   a  ++n + ++l++i+cHlGn
  NCBI__GCF_001579945.1:WP_066921191.1 137 PELPHVAVFDTAFHATLPPRAREYALPREVTERFGIRRYGFHGTSHAHVLSAACVHMNATPQELRIISCHLGN 209
                                           9999********************************************************************* PP

                             TIGR00016 217 GasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDl 289
                                           Gasv+a++ G+s++tsmG+tPLeGlvmGtR+GdiDp+++ +l +  g  ++++ e+ln ++Gl g++g ++D+
  NCBI__GCF_001579945.1:WP_066921191.1 210 GASVAAIEYGRSVETSMGMTPLEGLVMGTRCGDIDPGVLLHLLQSAGFDASALDELLNSRAGLTGLTG-TNDM 281
                                           ********************************************************************.**** PP

                             TIGR00016 290 RdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldl 362
                                           R+i+ + + g+e+++lA+++y+hRi+kyig+y+a + g ++ i FtgG+Gen+a vr++++++l++lG  ld+
  NCBI__GCF_001579945.1:WP_066921191.1 282 REIERRAARGDEHCRLAITLYAHRIRKYIGAYAAVMGG-VEVIAFTGGVGENSALVRHRCMQRLDFLGAVLDE 353
                                           ************************************76.********************************** PP

                             TIGR00016 363 elnnaa..rsgkesvisteeskvkvlviptneelviaeDalrl 403
                                           + n  a       + is+e s++++lv++ +ee++ia Da++l
  NCBI__GCF_001579945.1:WP_066921191.1 354 DANRDAgfDEFGVACISEEYSRTRLLVVRADEESAIAGDAAEL 396
                                           ****99444445678*************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (611 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: 00:00:00.01
# Mc/sec: 21.33
//
[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