GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Lactobacillus shenzhenensis LY-73

Align Acetate kinase; Acetokinase; EC 2.7.2.1 (characterized)
to candidate WP_022530349.1 L248_RS11225 acetate kinase

Query= SwissProt::P37877
         (395 letters)



>NCBI__GCF_000469325.1:WP_022530349.1
          Length = 396

 Score =  392 bits (1007), Expect = e-114
 Identities = 202/394 (51%), Positives = 272/394 (69%), Gaps = 2/394 (0%)

Query: 1   MSKIIAINAGSSSLKFQLFEMPSETVLTKGLVERIGIADSVFTIS-VNGEKNTEVTDIPD 59
           M K++AINAGSS+LKFQ+  MP ET+L  G ++R     +V TI    G+K+    ++ D
Sbjct: 1   MPKVLAINAGSSTLKFQVIAMPEETLLASGGIDRASSPAAVLTIKDAQGQKHESRANLED 60

Query: 60  HAVAVKMLLNKLTEFGIIKDLNEIDGIGHRVVHGGEKFSDSVLLTDETIKEIEDISELAP 119
              AV  LL  L   G++    E+ GIGHRVV GGEKF+    +T + I++I  ++E AP
Sbjct: 61  IDQAVDTLLTTLVAQGVLSAPEELAGIGHRVVAGGEKFAAPTRVTPQVIQDIAALAEYAP 120

Query: 120 LHNPANIVGIKAFKEVLPNVPAVAVFDTAFHQTMPEQSYLYSLPYEYYEKFGIRKYGFHG 179
           LHNP+    I AF + LP VP VAVFDTAFHQTMP  +YLYS+P +YY  +G R+YG HG
Sbjct: 121 LHNPSEAAYIAAFTKRLPGVPEVAVFDTAFHQTMPRVNYLYSIPMQYYRDYGARRYGAHG 180

Query: 180 TSHKYVTERAAELLGRPLKDLRLISCHLGNGASIAAVEGGKSIDTSMGFTPLAGVAMGTR 239
           TSH YV   AA+LL R L DL+LI+ HLGNGAS AA+  G+S+DTSMGFTPLAG+ MGTR
Sbjct: 181 TSHAYVAREAAKLLHRDLADLKLITLHLGNGASAAAITHGESLDTSMGFTPLAGLTMGTR 240

Query: 240 SGNIDPALIPYIMEKTGQTADEVLNTLNKKSGLLGISGFSSDLRDIVEATKEGNERAETA 299
           SG+IDP+L+ Y+  KT Q+  +++  LN +SG+LG++G SSD RDI  A + GNERA   
Sbjct: 241 SGDIDPSLVAYLAGKTHQSFQDMVQVLNDQSGMLGLTGLSSDFRDIDAAAQAGNERAILG 300

Query: 300 LEVFASRIHKYIGSYAARMSGVDAIIFTAGIGENSVEVRERVLRGLEFMGVYWDPALNNV 359
             +F +R+ KYIG+Y A M G+DAI+FT G+GE+   +R  VLR L +MG+  DPA  N 
Sbjct: 301 ERIFVNRVVKYIGAYTAEMGGLDAIVFTGGVGEHRGSLRHGVLRQLAYMGMTEDPAQVNA 360

Query: 360 RGEEAFISYPHSPVKVMIIPTDEEVMIARDVVRL 393
           +   AF++ P + V+ ++I T+EEVMIAR V++L
Sbjct: 361 QA-TAFLTTPEARVQALVITTNEEVMIARSVMKL 393


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: 392
Number of extensions: 15
Number of successful extensions: 3
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: 396
Length adjustment: 31
Effective length of query: 364
Effective length of database: 365
Effective search space:   132860
Effective search space used:   132860
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_022530349.1 L248_RS11225 (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.479566.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-143  462.4   0.0   6.5e-143  462.2   0.0    1.0  1  NCBI__GCF_000469325.1:WP_022530349.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000469325.1:WP_022530349.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.2   0.0  6.5e-143  6.5e-143       4     404 ..       2     394 ..       1     395 [. 0.98

  Alignments for each domain:
  == domain 1  score: 462.2 bits;  conditional E-value: 6.5e-143
                             TIGR00016   4 kkilvlnaGssslkfalldaensekvllsglverikleeariktvedgekkeeeklaiedheeavkkllntlk 76 
                                            k+l +naGss lkf+++ + + e++l+sg ++r  ++ a+++++  +++k+e   + ed ++av++ll+tl+
  NCBI__GCF_000469325.1:WP_022530349.1   2 PKVLAINAGSSTLKFQVIAMPE-ETLLASGGIDRASSPAAVLTIKDAQGQKHESRANLEDIDQAVDTLLTTLV 73 
                                           69*******************5.99***************9999999999*********************** PP

                             TIGR00016  77 kdkkilkelseialiGHRvvhGgekftesvivtdevlkkikdiselAPlHnpaelegieavlklkvllkaknv 149
                                           + + +l   +e+a iGHRvv Ggekf+  + vt +v+++i+ ++e+APlHnp+e+  i a++  k l+ +++v
  NCBI__GCF_000469325.1:WP_022530349.1  74 A-QGVLSAPEELAGIGHRVVAGGEKFAAPTRVTPQVIQDIAALAEYAPLHNPSEAAYIAAFT--KRLPGVPEV 143
                                           5.99**********************************************************..99999**** PP

                             TIGR00016 150 avFDtafHqtipeeaylYalPyslykelgvRrYGfHGtshkyvtqraakllnkplddlnlivcHlGnGasvsa 222
                                           avFDtafHqt+p+ +ylY++P+++y+++g RrYG+HGtsh yv+++aakll + l+dl+li++HlGnGas +a
  NCBI__GCF_000469325.1:WP_022530349.1 144 AVFDTAFHQTMPRVNYLYSIPMQYYRDYGARRYGAHGTSHAYVAREAAKLLHRDLADLKLITLHLGNGASAAA 216
                                           ************************************************************************* PP

                             TIGR00016 223 vknGksidtsmGltPLeGlvmGtRsGdiDpaiisylaetlglsldeieetlnkksGllgisglssDlRdildk 295
                                           +  G+s+dtsmG+tPL+Gl mGtRsGdiDp+++ yla ++ +s ++++++ln +sG+lg++glssD+Rdi ++
  NCBI__GCF_000469325.1:WP_022530349.1 217 ITHGESLDTSMGFTPLAGLTMGTRSGDIDPSLVAYLAGKTHQSFQDMVQVLNDQSGMLGLTGLSSDFRDIDAA 289
                                           ************************************************************************* PP

                             TIGR00016 296 keegneeaklAlkvyvhRiakyigkyiaslegelDaivFtgGiGenaaevrelvleklevlGlkldlelnnaa 368
                                            ++gne+a l  +++v+R+ kyig+y+a++ g lDaivFtgG+Ge   ++r+ vl++l+ +G+  d+++ n  
  NCBI__GCF_000469325.1:WP_022530349.1 290 AQAGNERAILGERIFVNRVVKYIGAYTAEMGG-LDAIVFTGGVGEHRGSLRHGVLRQLAYMGMTEDPAQVN-- 359
                                           ******************************76.**********************************9998.. PP

                             TIGR00016 369 rsgkesvisteeskvkvlviptneelviaeDalrla 404
                                             +  ++++t+e++v++lvi tnee++ia+ +++l+
  NCBI__GCF_000469325.1:WP_022530349.1 360 -AQATAFLTTPEARVQALVITTNEEVMIARSVMKLT 394
                                           .78899**************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (405 nodes)
Target sequences:                          1  (396 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: 15.87
//
[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