GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Crocosphaera subtropica ATCC 51142

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_009547761.1 CCE_RS14640 phosphate acetyltransferase

Query= SwissProt::P77844
         (329 letters)



>NCBI__GCF_000017845.1:WP_009547761.1
          Length = 698

 Score =  367 bits (941), Expect = e-106
 Identities = 183/326 (56%), Positives = 241/326 (73%), Gaps = 2/326 (0%)

Query: 1   MSAELFENWLLKRARAEHSHIVLPEGDDDRILMAAHQLLDQDICDITILGDPVKIKERAT 60
           ++ ++F   L+++A+    HIVLPEG D RIL A   LL QDI DIT+LG+  +I+    
Sbjct: 369 ITPKMFTYNLIQKAKLNKRHIVLPEGKDPRILKAVATLLSQDIVDITVLGEKKRIERTIQ 428

Query: 61  ELGLHL--NTAYLVNPLTDPRLEEFAEQFAELRKSKSVTIDEAREIMKDISYFGTMMVHN 118
             G+ L  N   ++NPL+ P+L+++ +   ELRK K +T++ A++++ D+SYFGTMMV++
Sbjct: 429 SHGIQLDINNLKIINPLSSPKLDDYIKTLYELRKHKGITLENAKDMLMDVSYFGTMMVYS 488

Query: 119 GDADGMVSGAANTTAHTIKPSFQIIKTVPEASVVSSIFLMVLRGRLWAFGDCAVNPNPTA 178
           GDADGMVSGA +TT +TI+P+ QIIKT PE  +VSS+F M L  ++  +GDCA+NPNPTA
Sbjct: 489 GDADGMVSGAIHTTGNTIRPALQIIKTKPEYQLVSSVFFMCLGDKVLVYGDCAINPNPTA 548

Query: 179 EQLGEIAVVSAKTAAQFGIDPRVAILSYSTGNSGGGSDVDRAIDALAEARRLNPELCVDG 238
           EQL EIAV+SA+TA  FGI PRVA+LSYS+G SG G DV+R   A   A++  P+L  +G
Sbjct: 549 EQLAEIAVISAETAQTFGIFPRVALLSYSSGESGTGEDVERVKQATILAQKRRPDLLFEG 608

Query: 239 PLQFDAAVDPGVARKKMPDSDVAGQANVFIFPDLEAGNIGYKTAQRTGHALAVGPILQGL 298
           P+Q+DAAVD  VA +KMPDS+VAGQA VF+FPDL  GN  YK  QR   A+A+GPILQGL
Sbjct: 609 PIQYDAAVDKTVAAQKMPDSEVAGQATVFVFPDLNTGNNTYKAVQRETGAIAIGPILQGL 668

Query: 299 NKPVNDLSRGATVPDIVNTVAITAIQ 324
            KPVNDLSRG TV DI+NTV ITAIQ
Sbjct: 669 KKPVNDLSRGCTVEDIINTVVITAIQ 694


Lambda     K      H
   0.318    0.134    0.386 

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: 550
Number of extensions: 24
Number of successful extensions: 2
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: 329
Length of database: 698
Length adjustment: 33
Effective length of query: 296
Effective length of database: 665
Effective search space:   196840
Effective search space used:   196840
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate WP_009547761.1 CCE_RS14640 (phosphate acetyltransferase)
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))

# 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/TIGR00651.hmm
# target sequence database:        /tmp/gapView.1203392.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00651  [M=304]
Accession:   TIGR00651
Description: pta: phosphate acetyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.3e-134  431.6   0.1   1.4e-133  431.0   0.1    1.3  1  NCBI__GCF_000017845.1:WP_009547761.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017845.1:WP_009547761.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.0   0.1  1.4e-133  1.4e-133       1     304 []     389     692 ..     389     692 .. 1.00

  Alignments for each domain:
  == domain 1  score: 431.0 bits;  conditional E-value: 1.4e-133
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           ivlPEg+++r+lkA+a+l++++i++ ++l++k++++++ ++++++l+++++++++p +s+++++y+++lye+r
  NCBI__GCF_000017845.1:WP_009547761.1 389 IVLPEGKDPRILKAVATLLSQDIVDITVLGEKKRIERTiQSHGIQLDINNLKIINPLSSPKLDDYIKTLYELR 461
                                           8************************************999********************************* PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           khkG+t+++a+++l D +++++++v+ g adg+vsGa +tt +t+rpalqiikt++  +lvssvf+m+++++v
  NCBI__GCF_000017845.1:WP_009547761.1 462 KHKGITLENAKDMLMDVSYFGTMMVYSGDADGMVSGAIHTTGNTIRPALQIIKTKPEYQLVSSVFFMCLGDKV 534
                                           ************************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                           lv++DCa++++P+ae+LAeiA+ sa++a+++g + p+vallsys++ sg ge+ve+vk+A+ ++++++pdll+
  NCBI__GCF_000017845.1:WP_009547761.1 535 LVYGDCAINPNPTAEQLAEIAVISAETAQTFG-IFPRVALLSYSSGESGTGEDVERVKQATILAQKRRPDLLF 606
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           +G++q+DaA+ ++va++k+p+sevag+a+vfvFPdL++Gn++Yk+vqR+++a aiGPilqGl+kPvnDLsRG+
  NCBI__GCF_000017845.1:WP_009547761.1 607 EGPIQYDAAVDKTVAAQKMPDSEVAGQATVFVFPDLNTGNNTYKAVQRETGAIAIGPILQGLKKPVNDLSRGC 679
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +vedi+n+v+ita
  NCBI__GCF_000017845.1:WP_009547761.1 680 TVEDIINTVVITA 692
                                           ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (698 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 32.02
//
[ok]

This GapMind analysis is from Apr 09 2024. 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