Alignments for a candidate for ackA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for ackA in Pedobacter sp. GW460-11-11-14-LB5

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate CA265_RS10080 CA265_RS10080 acetate kinase

Query= BRENDA::P38502
         (408 letters)



>FitnessBrowser__Pedo557:CA265_RS10080
          Length = 398

 Score =  383 bits (983), Expect = e-111
 Identities = 199/398 (50%), Positives = 271/398 (68%), Gaps = 7/398 (1%)

Query: 1   MKVLVINAGSSSLKYQLIDMTNESALAVGLCERIGIDNSIITQKKFDGKK---LEKLTDL 57
           M +LVIN+GSSSLKYQL +M  ++ L  GL ERIGI+ S I    +   +   +E+   +
Sbjct: 1   MNILVINSGSSSLKYQLFNMPEKAPLCSGLVERIGIEGSFIKHSVYRNNEKYNIEQSGFI 60

Query: 58  PTHKDALEEVVKALTDDEFGVIKDMGEINAVGHRVVHGGEKFTTSALYDEGVEKAIKDCF 117
             H + L++V+  LT+ E+ VI    +I AVGHRVVHGGE FT + L  + V+  IK  F
Sbjct: 61  ANHGEGLKQVLALLTEGEYAVIASPDDIAAVGHRVVHGGEHFTGATLITDEVKHQIKKLF 120

Query: 118 ELAPLHNPPNMMGISACAEIMPGTPMVIVFDTAFHQTMPPYAYMYALPYDLYEKHGVRKY 177
            LAPLHNP N   I    +       + VFDTAFHQT+P  AY YA+P   Y++HG+R Y
Sbjct: 121 SLAPLHNPVNYKCIEVAEQTFVNAKQIAVFDTAFHQTIPEQAYRYAIPEWYYKEHGIRVY 180

Query: 178 GFHGTSHKYVAERAALMLGKPAEETKIITCHLGNGSSITAVEGGKSVETSMGFTPLEGLA 237
           GFHGTSHKYV+E+A   L K   E+KII+ HLGNG SITA++ GKS++TSMGF PL GL 
Sbjct: 181 GFHGTSHKYVSEQAIKWLNK--AESKIISIHLGNGCSITAIKNGKSIDTSMGFGPLSGLM 238

Query: 238 MGTRCGSIDPAIVPFLMEKEGLTTREIDTLMNKKSGVLGVSGLSNDFRDLDEAASKGNRK 297
           MGTR G IDP+++  LME  G T  ++ TL+NK+SG+LGV G S+D RD+ +  S+GN  
Sbjct: 239 MGTRSGDIDPSVIFHLMEHSGYTLEQLSTLVNKQSGLLGVGG-SSDMRDIRKMVSEGNAA 297

Query: 298 AELALEIFAYKVKKFIGEYSAVLNGADAVVFTAGIGENSASIRKRILTGLDGIGIKIDDE 357
           A LAL+++AY++KKFIG Y+A+LNG DA+VFTAG+GEN +++R+ + + LD +GI++D  
Sbjct: 298 AILALKLYAYRIKKFIGAYAAILNGIDAIVFTAGVGENDSNMREAVCSALDYLGIELDPN 357

Query: 358 KN-KIRGQEIDISTPDAKVRVFVIPTNEELAIARETKE 394
           +N    G   +I+   AKV++ VIPTNEE  IA +  E
Sbjct: 358 QNAAYHGALKEINKTGAKVKILVIPTNEEYEIAHQCFE 395


Lambda     K      H
   0.316    0.135    0.380 

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: 442
Number of extensions: 14
Number of successful extensions: 5
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: 408
Length of database: 398
Length adjustment: 31
Effective length of query: 377
Effective length of database: 367
Effective search space:   138359
Effective search space used:   138359
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 CA265_RS10080 CA265_RS10080 (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.20331.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   8.3e-154  498.1   1.8   9.2e-154  497.9   1.8    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS10080  CA265_RS10080 acetate kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS10080  CA265_RS10080 acetate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.9   1.8  9.2e-154  9.2e-154       4     401 ..       1     394 [.       1     398 [] 0.95

  Alignments for each domain:
  == domain 1  score: 497.9 bits;  conditional E-value: 9.2e-154
                                  TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktv..edgekke.eeklaiedheeav 68 
                                                + ilv+n+Gssslk++l+++ + +  l+sglveri +e+++ik     ++ek + e+   i++h e++
  lcl|FitnessBrowser__Pedo557:CA265_RS10080   1 MNILVINSGSSSLKYQLFNMPE-KAPLCSGLVERIGIEGSFIKHSvyRNNEKYNiEQSGFIANHGEGL 67 
                                                579******************5.7779*************9997643444444413445579****** PP

                                  TIGR00016  69 kkllntlkk.dkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegie 135
                                                k++l  l++ + +++ + ++ia++GHRvvhGge+ft ++++tdev ++ik++ +lAPlHnp + + ie
  lcl|FitnessBrowser__Pedo557:CA265_RS10080  68 KQVLALLTEgEYAVIASPDDIAAVGHRVVHGGEHFTGATLITDEVKHQIKKLFSLAPLHNPVNYKCIE 135
                                                ********999********************************************************* PP

                                  TIGR00016 136 avlklkvllkaknvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkp 203
                                                 +   ++ ++ak++avFDtafHqtipe+ay Ya+P+ +yke+g+R YGfHGtshkyv+++a k lnk 
  lcl|FitnessBrowser__Pedo557:CA265_RS10080 136 VAE--QTFVNAKQIAVFDTAFHQTIPEQAYRYAIPEWYYKEHGIRVYGFHGTSHKYVSEQAIKWLNK- 200
                                                ***..6778899*******************************************************. PP

                                  TIGR00016 204 lddlnlivcHlGnGasvsavknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeiee 271
                                                 +++++i++HlGnG s++a+knGksidtsmG+ PL Gl+mGtRsGdiDp++i++l+e+ g +l+++ +
  lcl|FitnessBrowser__Pedo557:CA265_RS10080 201 -AESKIISIHLGNGCSITAIKNGKSIDTSMGFGPLSGLMMGTRSGDIDPSVIFHLMEHSGYTLEQLST 267
                                                .999**************************************************************** PP

                                  TIGR00016 272 tlnkksGllgisglssDlRdildkkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiG 339
                                                ++nk+sGllg+ g ssD+Rdi + ++egn  a lAlk+y++Ri+k+ig+y+a l+g +DaivFt+G+G
  lcl|FitnessBrowser__Pedo557:CA265_RS10080 268 LVNKQSGLLGVGG-SSDMRDIRKMVSEGNAAAILALKLYAYRIKKFIGAYAAILNG-IDAIVFTAGVG 333
                                                *************.****************************************88.*********** PP

                                  TIGR00016 340 enaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlviptneelviaeDal 401
                                                en++++re v+++l+ lG++ld+++n  a +g  + i+++ +kvk+lviptnee  ia+ ++
  lcl|FitnessBrowser__Pedo557:CA265_RS10080 334 ENDSNMREAVCSALDYLGIELDPNQNA-AYHGALKEINKTGAKVKILVIPTNEEYEIAHQCF 394
                                                **************************9.8999999***********************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (398 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: 6.70
//
[ok]

This GapMind analysis is from Sep 17 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, or view the source code.

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