Aligments for a candidate for ackA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for ackA in Dinoroseobacter shibae DFL-12

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate 3607216 Dshi_0632 acetate kinase (RefSeq)

Query= curated2:B8EIS2
         (404 letters)



>FitnessBrowser__Dino:3607216
          Length = 382

 Score =  410 bits (1055), Expect = e-119
 Identities = 214/394 (54%), Positives = 277/394 (70%), Gaps = 17/394 (4%)

Query: 5   VITLNAGSSSIKFALFREGLTQEGSAKELTPMAIGLAEMVGEERRITVHDGAGAKIYEVK 64
           ++TLNAGSSS+KFA++        +A     +  G  + +G   R+ V+     K     
Sbjct: 4   LLTLNAGSSSVKFAVYE-------AANAPLLIVAGEVDGLGPAARLIVNTNPATK----- 51

Query: 65  RTEHVDAPFHAEALRRILAWRQSAFPDAEVVAAGHRVVHGGVHYSAPVIVTDEVLKYLHT 124
               +    HA AL  ILA  +      +VV  GHR+VHGG  ++APV +T +V++ L  
Sbjct: 52  --RDLGPTDHAAALHAILAALRPILSGRQVVGVGHRIVHGGGAFTAPVELTPDVIEALEA 109

Query: 125 LIPLAPLHEPYNIAGILGAREAWPHVEQVACFDTAFHRTHPFVNDVFALPRRFYDEGVRR 184
            +PLAPLH+P+N+A +  AR+A+P   Q+ CFDTAFH  HP+VND FALPRRFY+ GVRR
Sbjct: 110 FVPLAPLHQPHNLAMVAAARQAFPDAVQIGCFDTAFHAGHPWVNDTFALPRRFYEAGVRR 169

Query: 185 YGFHGLSYEYIVRRLREIAPLHAAGRVVVAHLGNGASMCAIRDGLSVASSMGFTALDGLP 244
           YGFHGLSY+YI  +LR   P  AAGRVV+AHLGNGASMCA+RDG SV S+MGF+ALDGLP
Sbjct: 170 YGFHGLSYDYITDKLRADCPELAAGRVVIAHLGNGASMCAVRDGRSVGSTMGFSALDGLP 229

Query: 245 MGTRCGQLDPGVVLYLMQEKKMSAAEITDLLYRESGLKGLSGLSHDMRELEAADTLEAQQ 304
           MGTRCGQLDPGV+LY+M E+ MS  EIT +LY ESGL+GLSG SHDMR L+A+D   A +
Sbjct: 230 MGTRCGQLDPGVLLYMM-EQGMSREEITSILYEESGLQGLSGFSHDMRTLQASDDPRAAE 288

Query: 305 AIEYFVFRIRRELGGLAAVLKGIDAIVFCGGIGENSRHVRERVLEGMEWIGVELDRSANS 364
           AI+Y+VFRIRRELG + AVL GIDA+VFCGGIGEN+  +R RV+EGM+++G+ LD  AN+
Sbjct: 289 AIDYYVFRIRRELGAMTAVLGGIDALVFCGGIGENAAVIRARVIEGMDYLGLSLDAEANA 348

Query: 365 ANAEVISSERSRTRVFVIPTDEEGMIARHTLALL 398
            NA  +++      + VIPT+EE +IAR   A L
Sbjct: 349 RNATRVAT--GPVPILVIPTNEELVIARAVSAAL 380


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: 467
Number of extensions: 15
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: 404
Length of database: 382
Length adjustment: 31
Effective length of query: 373
Effective length of database: 351
Effective search space:   130923
Effective search space used:   130923
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 3607216 Dshi_0632 (acetate kinase (RefSeq))
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.9980.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-107  346.1   0.0   1.4e-107  345.9   0.0    1.0  1  lcl|FitnessBrowser__Dino:3607216  Dshi_0632 acetate kinase (RefSeq


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3607216  Dshi_0632 acetate kinase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  345.9   0.0  1.4e-107  1.4e-107       4     400 ..       2     376 ..       1     381 [. 0.92

  Alignments for each domain:
  == domain 1  score: 345.9 bits;  conditional E-value: 1.4e-107
                         TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlkkdkk 80 
                                       +++l lnaGsss+kfa+++a+n+  +++ g v+ +  +     +v+++   ++  l  +dh++a++++l +l     
  lcl|FitnessBrowser__Dino:3607216   2 SVLLTLNAGSSSVKFAVYEAANAPLLIVAGEVDGLGPAAR--LIVNTN-PATKRDLGPTDHAAALHAILAALRP--- 72 
                                       57899*****************9999*******9988777..434444.5666678889**************6... PP

                         TIGR00016  81 ilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknvavFDtafH 157
                                        + +  ++  +GHR+vhGg  ft  v +t +v+++++ +++lAPlH p +l  + a+   +  ++a ++ +FDtafH
  lcl|FitnessBrowser__Dino:3607216  73 -ILSGRQVVGVGHRIVHGGGAFTAPVELTPDVIEALEAFVPLAPLHQPHNLAMVAAAR--QAFPDAVQIGCFDTAFH 146
                                       .56778999************************************************9..5667788********** PP

                         TIGR00016 158 qtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsavknGksidtsmG 234
                                          p  +  +alP+++y e gvRrYGfHG+s+ y+t+++       l+  +++++HlGnGas++av++G+s+  +mG
  lcl|FitnessBrowser__Dino:3607216 147 AGHPWVNDTFALPRRFY-EAGVRRYGFHGLSYDYITDKLRADCPE-LAAGRVVIAHLGNGASMCAVRDGRSVGSTMG 221
                                       *************9888.58*******************999887.8999*************************** PP

                         TIGR00016 235 ltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildkkeegneeaklAlkvyv 311
                                       +  L+Gl mGtR+G++Dp+++ y++e +g+s +ei+++l  +sGl g+sg+s D+R++ +     + +a+ A++ yv
  lcl|FitnessBrowser__Dino:3607216 222 FSALDGLPMGTRCGQLDPGVLLYMME-QGMSREEITSILYEESGLQGLSGFSHDMRTLQASD---DPRAAEAIDYYV 294
                                       ************************98.59****************************98766...7789******** PP

                         TIGR00016 312 hRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaarsgkesvisteeskvkvlvi 388
                                        Ri++ +g+++a l g +Da+vF gGiGenaa +r++v+e+++ lGl ld e n      + + ++   + v +lvi
  lcl|FitnessBrowser__Dino:3607216 295 FRIRRELGAMTAVLGG-IDALVFCGGIGENAAVIRARVIEGMDYLGLSLDAEANA----RNATRVA--TGPVPILVI 364
                                       **************76.*************************************9....3333444..599****** PP

                         TIGR00016 389 ptneelviaeDa 400
                                       ptneelvia+ +
  lcl|FitnessBrowser__Dino:3607216 365 PTNEELVIARAV 376
                                       ********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (382 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: 7.36
//
[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