Alignments for a candidate for ackA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Halomonas desiderata SP1

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_086512003.1 BZY95_RS21880 acetate kinase

Query= BRENDA::E3W769
         (401 letters)



>NCBI__GCF_002151265.1:WP_086512003.1
          Length = 392

 Score =  370 bits (949), Expect = e-107
 Identities = 196/388 (50%), Positives = 264/388 (68%), Gaps = 10/388 (2%)

Query: 6   VLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAFTAHRE 65
           VLV+NCGSSS+K+A++       ++SGLAE  G  D+R+K   + G++  +  A   H  
Sbjct: 5   VLVINCGSSSIKYALVPKDPSRPRLSGLAERLGNGDARLKGTDSHGESFEQALAGADHAR 64

Query: 66  AVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASLAPLHN 125
           A+E  I+  +    P       A+GHRIVHGGE+FTR+ +I  EV+  IE  A+LAPLHN
Sbjct: 65  ALEA-ILERLEGRLPV------AVGHRIVHGGERFTRAALIDDEVVAAIEQTAALAPLHN 117

Query: 126 PAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGMHGTSH 185
           PA+L G+ A    FP LPQV VFDTAFHQ++P +AY YALP  LYREH IRRYG HGTSH
Sbjct: 118 PANLTGLAATRRLFPDLPQVAVFDTAFHQSLPPRAYRYALPESLYREHGIRRYGFHGTSH 177

Query: 186 FYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMGTRCGD 245
            YV R A  + G  ++    + AHLGNG S  A+  G+S+DTSMGLTPLEGL MGTR GD
Sbjct: 178 AYVSRRADALSG--LEGGGWLTAHLGNGCSACAVWKGQSLDTSMGLTPLEGLAMGTRSGD 235

Query: 246 LDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGATLALDI 305
           +DP +  HL +QLG++L+ ++ +LN++SGLLG+S LTND R +E    DGH GATLA+++
Sbjct: 236 VDPGLHAHLSRQLGWSLERIDEVLNRESGLLGLSGLTNDMRELEAAEADGHPGATLAIEV 295

Query: 306 FCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILNKAARF 365
           FCYR+AK +A+ +  L RLD ++FTGGIGENS+L+RE+V  LL  F  +++  +N     
Sbjct: 296 FCYRIAKSLAALSCALPRLDGLVFTGGIGENSSLVRERVTALLPHFGLQLNRTVNSETIR 355

Query: 366 GQQGVITQAGTPIAMVIPTNEEWVIAED 393
           G++G I   G  +  VIPT+EE  IA +
Sbjct: 356 GKEGRIDAGGRQL-WVIPTDEEGQIATE 382


Lambda     K      H
   0.321    0.139    0.409 

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: 465
Number of extensions: 18
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: 401
Length of database: 392
Length adjustment: 31
Effective length of query: 370
Effective length of database: 361
Effective search space:   133570
Effective search space used:   133570
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_086512003.1 BZY95_RS21880 (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.4088.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.5e-129  417.5   0.0     3e-129  417.2   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086512003.1  BZY95_RS21880 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086512003.1  BZY95_RS21880 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.2   0.0    3e-129    3e-129       4     400 ..       3     383 ..       1     388 [. 0.95

  Alignments for each domain:
  == domain 1  score: 417.2 bits;  conditional E-value: 3e-129
                                 TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkll 72 
                                               + +lv+n+Gsss+k+al+ +   ++  lsgl+er+   +ar+k   + ++  e+ la +dh++a++++l
  lcl|NCBI__GCF_002151265.1:WP_086512003.1   3 TSVLVINCGSSSIKYALVPKDP-SRPRLSGLAERLGNGDARLKGTDSHGESFEQALAGADHARALEAIL 70 
                                               679***************9985.55559***************999999999***************** PP

                                 TIGR00016  73 ntlkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklk 141
                                               ++l+             ++GHR+vhGge+ft +++++dev+++i++ + lAPlHnpa+l+g+ a     
  lcl|NCBI__GCF_002151265.1:WP_086512003.1  71 ERLEGRL--------PVAVGHRIVHGGERFTRAALIDDEVVAAIEQTAALAPLHNPANLTGLAATR--R 129
                                               ****622........3479*********************************************99..5 PP

                                 TIGR00016 142 vllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnli 210
                                                 ++ ++vavFDtafHq +p +ay YalP+sly+e+g+RrYGfHGtsh yv++ra+ l +   +    +
  lcl|NCBI__GCF_002151265.1:WP_086512003.1 130 LFPDLPQVAVFDTAFHQSLPPRAYRYALPESLYREHGIRRYGFHGTSHAYVSRRADALSGL--EGGGWL 196
                                               566778************************************************9998887..9999** PP

                                 TIGR00016 211 vcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGl 279
                                               ++HlGnG s +av +G+s+dtsmGltPLeGl+mGtRsGd+Dp++  +l+ +lg sl+ i e+ln++sGl
  lcl|NCBI__GCF_002151265.1:WP_086512003.1 197 TAHLGNGCSACAVWKGQSLDTSMGLTPLEGLAMGTRSGDVDPGLHAHLSRQLGWSLERIDEVLNRESGL 265
                                               ********************************************************************* PP

                                 TIGR00016 280 lgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrel 348
                                               lg+sgl++D+R+++++ ++g+  a+lA++v+++Riak +++   +l  +lD++vFtgGiGen++ vre+
  lcl|NCBI__GCF_002151265.1:WP_086512003.1 266 LGLSGLTNDMRELEAAEADGHPGATLAIEVFCYRIAKSLAALSCALP-RLDGLVFTGGIGENSSLVRER 333
                                               **********************************************5.5******************** PP

                                 TIGR00016 349 vleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDa 400
                                               v   l  +Gl+l+   n  + +gke+ i    +  ++ vipt+ee  ia ++
  lcl|NCBI__GCF_002151265.1:WP_086512003.1 334 VTALLPHFGLQLNRTVNSETIRGKEGRID--AGGRQLWVIPTDEEGQIATET 383
                                               ***************************98..788999***********9876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 7.62
//
[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