GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Collimonas arenae Ter10

Align Probable propionate kinase; EC 2.7.2.15 (characterized)
to candidate WP_061533398.1 CAter10_RS10715 acetate/propionate family kinase

Query= SwissProt::P74879
         (404 letters)



>NCBI__GCF_001584165.1:WP_061533398.1
          Length = 406

 Score =  258 bits (658), Expect = 3e-73
 Identities = 163/395 (41%), Positives = 223/395 (56%), Gaps = 13/395 (3%)

Query: 5   IMAINAGSSSLKFQLLEMPQGDMLCQ----GLIERIGMADAQVTIKTHSQKWQETVPVAD 60
           I+ +N GSSS+KF L +     +  Q    G ++ IG   + +   T S        V  
Sbjct: 14  ILVLNCGSSSIKFALFDTSPAVLARQADWKGKVDGIGGKPSYIESGTESAPLALGT-VQP 72

Query: 61  HRDAVTLLLEKLLGYQIINSLRDIDGVGHRVAHGGEFFKDSTLVTDETLAQIERLAELAP 120
           + DA+  + E++  +      R +  V HRV HGG  +   T +  E LA ++    LAP
Sbjct: 73  YHDALMHIRERVALHL---GARRLCAVAHRVVHGGSKYSAPTRIDAEVLADLKNYIPLAP 129

Query: 121 LHNPVNALGIHVFRQLLPDAPSVAVFDTAFHQTLDEPAYIYPLPWHYYAELGIRRYGFHG 180
           LH P     I V     P    VA FDTAFH TL     + PLP H   E G+RRYGFHG
Sbjct: 130 LHQPFALEAIEVLLSSQPGLLQVACFDTAFHHTLPHVEQMLPLP-HALWERGLRRYGFHG 188

Query: 181 TSHKYVSGVLAEKLGVPLSALRVICCHLGNGSSICAIKNGRSVNTSMGFTPQSGVMMGTR 240
            S++Y+S VL E+ G   S  RVI  HLG+G+S+CA++  RSV T+MGF+   G+MMGTR
Sbjct: 189 LSYEYMSVVLEERFGAA-SHGRVIAAHLGSGASLCAMRALRSVGTTMGFSALDGLMMGTR 247

Query: 241 SGDIDPSILPWIAQRESKTPQQLNQLLNNESGLLGVSGVSSDYRDV---EQAANTGNRQA 297
            G +DP  + ++ + E  + +Q+  LL +ESGLLGVSG SSD   +   EQ  +    + 
Sbjct: 248 CGALDPGAVLYLMEIEKLSLEQVAHLLYHESGLLGVSGFSSDPPVLFAQEQRQDAVGDRV 307

Query: 298 KLALTLFAERIRATIGSYIMQMGGLDALVFTGGIGENSARARSAVCHNLQFLGLAVDEEK 357
           + AL L+  RI   IG+    +GGLD LVFT GIGE+SA  RS VC +L FLG+ +D+E 
Sbjct: 308 RAALDLYVRRIVREIGALAAVLGGLDLLVFTAGIGEHSAEIRSRVCRDLAFLGVGLDQES 367

Query: 358 NQRNATFIQTENALVKVAVINTNEELMIAQDVMRI 392
           NQRNA FI   ++ V VAV  TNEE + A+  + I
Sbjct: 368 NQRNAPFISLVDSRVTVAVEPTNEEWIAARHTLAI 402


Lambda     K      H
   0.319    0.135    0.392 

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: 355
Number of extensions: 20
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: 406
Length adjustment: 31
Effective length of query: 373
Effective length of database: 375
Effective search space:   139875
Effective search space used:   139875
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_061533398.1 CAter10_RS10715 (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.3864870.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.8e-106  339.8   0.0   1.2e-105  339.5   0.0    1.0  1  NCBI__GCF_001584165.1:WP_061533398.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001584165.1:WP_061533398.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.5   0.0  1.2e-105  1.2e-105       5     401 ..      13     400 ..      10     404 .. 0.91

  Alignments for each domain:
  == domain 1  score: 339.5 bits;  conditional E-value: 1.2e-105
                             TIGR00016   5 kilvlnaGssslkfalldaen...sekvllsglverikleeariktvedgekkeeeklaiedheeavkkllnt 74 
                                            ilvln+Gsss+kfal+d++    +++  ++g v+ i  + + i   + +e    +   ++ ++ a+ ++ ++
  NCBI__GCF_001584165.1:WP_061533398.1  13 FILVLNCGSSSIKFALFDTSPavlARQADWKGKVDGIGGKPSYIE--SGTESAPLALGTVQPYHDALMHIRER 83 
                                           59****************997555667789*******99999554..444456677888999*******9999 PP

                             TIGR00016  75 lkkdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkak 147
                                           +     ++     + ++ HRvvhGg+k++  + +++evl+++k+ ++lAPlH p +le+ie +l    ++   
  NCBI__GCF_001584165.1:WP_061533398.1  84 VA----LHLGARRLCAVAHRVVHGGSKYSAPTRIDAEVLADLKNYIPLAPLHQPFALEAIEVLL--SSQPGLL 150
                                           98....466788999*************************************************..5566666 PP

                             TIGR00016 148 nvavFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasv 220
                                           +va+FDtafH+t+p+   + +lP+ l++  g+RrYGfHG+s++y++  +++ ++  + + ++i +HlG Gas+
  NCBI__GCF_001584165.1:WP_061533398.1 151 QVACFDTAFHHTLPHVEQMLPLPHALWE-RGLRRYGFHGLSYEYMSVVLEERFGA-ASHGRVIAAHLGSGASL 221
                                           ***********************88885.79***********************9.7899************* PP

                             TIGR00016 221 savknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdil 293
                                           +a++  +s+ t+mG+  L+Gl+mGtR+G +Dp+++ yl+e ++lsl+++ ++l  +sGllg+sg+ssD  +++
  NCBI__GCF_001584165.1:WP_061533398.1 222 CAMRALRSVGTTMGFSALDGLMMGTRCGALDPGAVLYLMEIEKLSLEQVAHLLYHESGLLGVSGFSSDPPVLF 294
                                           ********************************************************************99988 PP

                             TIGR00016 294 dkke...egneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldle 363
                                           ++ +   +  ++ + Al++yv Ri + ig+ +a l g lD +vFt+GiGe +ae+r +v+++l++lG+ ld+e
  NCBI__GCF_001584165.1:WP_061533398.1 295 AQEQrqdAVGDRVRAALDLYVRRIVREIGALAAVLGG-LDLLVFTAGIGEHSAEIRSRVCRDLAFLGVGLDQE 366
                                           766521145578999********************76.*********************************** PP

                             TIGR00016 364 lnnaarsgkesvisteeskvkvlviptneelviaeDal 401
                                            n+     +  +is  +s+v+v+v ptnee++ a+ +l
  NCBI__GCF_001584165.1:WP_061533398.1 367 SNQ----RNAPFISLVDSRVTVAVEPTNEEWIAARHTL 400
                                           *99....7789********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (406 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.50
//
[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:

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