GapMind for catabolism of small carbon sources

 

Alignments 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.5660.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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.44
//
[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:

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:

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:

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:

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