GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Lactobacillus oryzae SG293

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_034525905.1 LOSG293_RS00890 acetate/propionate family kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_000740055.1:WP_034525905.1
          Length = 400

 Score =  345 bits (884), Expect = 2e-99
 Identities = 172/396 (43%), Positives = 263/396 (66%), Gaps = 5/396 (1%)

Query: 1   MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTISVNGEKNTEVTDIPDH 60
           M K + INAGSSSLK++LF++P+ETV+ +GLVERI + DS+  ++  G K+ E  +    
Sbjct: 1   MKKYLVINAGSSSLKWKLFDIPAETVIAEGLVERINLEDSIVKLAYRGNKSKETVERLSM 60

Query: 61  AVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAPL 120
           + AVK +L  L +  II  L++I  +GHR+V G E+F  +  L    I  ++ +S+ APL
Sbjct: 61  SDAVKSVLRVLVDRKIISRLSDIHAVGHRIVAGAEQFKSATKLDQRAIASLKQLSDYAPL 120

Query: 121 HNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHGT 180
           HNP  +  ++     LPN P  AVFD+  +  M +++ L+ +PYE  ++F IR+YG HG 
Sbjct: 121 HNPMQVATVELLATYLPNAPQFAVFDSQLYLQMADETALFGIPYELSKEFHIRRYGEHGI 180

Query: 181 SHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTRS 240
           SH+Y+  + A L+ RPL +L +++ HLG+GAS++A + GK  DTSMG TP+ GV MGTRS
Sbjct: 181 SHEYLACQTATLMKRPLNELNIVTLHLGSGASVSAFKNGKIYDTSMGLTPVTGVLMGTRS 240

Query: 241 GNIDPALIPYIMEKTG-QTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETA 299
           G++DPA++P++M++    +++ VL  LN+KSGL G+SG SSD+RD+V +    +ERA  A
Sbjct: 241 GDVDPAIVPFLMKRLQLDSSEAVLALLNEKSGLHGVSGISSDMRDLVAS---DSERANLA 297

Query: 300 LEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNV 359
           L++F +++ K IG+Y A M G+DAI F  GIGE   ++R R++  +  +GV  DP LN++
Sbjct: 298 LQMFENQVVKQIGAYFAEMGGIDAITFAGGIGEKDSDMRRRIMTRVSHLGVRMDPNLNDL 357

Query: 360 RGEEAFISYPHSPVKVMIIPTDEEVMIARDVVRLAK 395
            G E  I+ P SP+  +I+PT+EE+ I R V    K
Sbjct: 358 -GVEGRITIPTSPIMALIVPTNEELAIVRQVAEQLK 392


Lambda     K      H
   0.317    0.136    0.381 

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: 373
Number of extensions: 18
Number of successful extensions: 4
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: 395
Length of database: 400
Length adjustment: 31
Effective length of query: 364
Effective length of database: 369
Effective search space:   134316
Effective search space used:   134316
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 WP_034525905.1 LOSG293_RS00890 (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.591203.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.4e-128  412.5   0.1   9.5e-128  412.3   0.1    1.0  1  NCBI__GCF_000740055.1:WP_034525905.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000740055.1:WP_034525905.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.3   0.1  9.5e-128  9.5e-128       4     401 ..       2     388 ..       1     392 [. 0.96

  Alignments for each domain:
  == domain 1  score: 412.3 bits;  conditional E-value: 9.5e-128
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                           kk lv+naGssslk++l+d   +e+v+++glveri+le++++k    g +k++e+++  + + avk +l+ l+
  NCBI__GCF_000740055.1:WP_034525905.1   2 KKYLVINAGSSSLKWKLFDIP-AETVIAEGLVERINLEDSIVKLAYRG-NKSKETVERLSMSDAVKSVLRVLV 72 
                                           789******************.7*****************77755555.77888899999************* PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                            d+ki+  ls+i+++GHR+v G+e+f++++ +++ +++++k++s++APlHnp ++ ++e +   + l++a++ 
  NCBI__GCF_000740055.1:WP_034525905.1  73 -DRKIISRLSDIHAVGHRIVAGAEQFKSATKLDQRAIASLKQLSDYAPLHNPMQVATVELLA--TYLPNAPQF 142
                                           .8*********************************************************999..99******* PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           avFD   +  +++e++l+++Py+l ke+ +RrYG HG+sh+y++ ++a l+ +pl++ln++++HlG Gasvsa
  NCBI__GCF_000740055.1:WP_034525905.1 143 AVFDSQLYLQMADETALFGIPYELSKEFHIRRYGEHGISHEYLACQTATLMKRPLNELNIVTLHLGSGASVSA 215
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlgl.sldeieetlnkksGllgisglssDlRdild 294
                                            knGk +dtsmGltP+ G++mGtRsGd+Dpai+ +l+++l+l s +++  +ln ksGl g+sg+ssD+Rd+++
  NCBI__GCF_000740055.1:WP_034525905.1 216 FKNGKIYDTSMGLTPVTGVLMGTRSGDVDPAIVPFLMKRLQLdSSEAVLALLNEKSGLHGVSGISSDMRDLVA 288
                                           ************************************9998763788899**********************98 PP

                             TIGR00016 295 kkeegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnna 367
                                                 e+a+lAl+++ + + k ig+y a++ g +Dai F gGiGe ++++r++++ ++  lG+++d++ln  
  NCBI__GCF_000740055.1:WP_034525905.1 289 SD---SERANLALQMFENQVVKQIGAYFAEMGG-IDAITFAGGIGEKDSDMRRRIMTRVSHLGVRMDPNLND- 356
                                           87...6789**********************76.*************************************9. PP

                             TIGR00016 368 arsgkesvisteeskvkvlviptneelviaeDal 401
                                              g e+ i+ + s + +l++ptneel+i++ ++
  NCBI__GCF_000740055.1:WP_034525905.1 357 --LGVEGRITIPTSPIMALIVPTNEELAIVRQVA 388
                                           ..89999***********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (400 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: 24.27
//
[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