GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Halomonas xinjiangensis TRM 0175

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_043530028.1 JH15_RS10540 phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>NCBI__GCF_000759345.1:WP_043530028.1
          Length = 727

 Score =  791 bits (2042), Expect = 0.0
 Identities = 417/713 (58%), Positives = 524/713 (73%), Gaps = 21/713 (2%)

Query: 3   TFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTHGL 62
           T  + PT  G GLTS  LGL++AL+  GLK GF KP  Q      GP+RSS LVAR   L
Sbjct: 12  TLLMVPTAVGTGLTSACLGLIKALDSIGLKAGFLKPFMQQELNGPGPDRSSALVARAMNL 71

Query: 63  DTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADK----DVVIVEGMVPTRHASYAA 118
             P  +P  ++ER L + +LDELLE ++ L+Q+AA D+    D+V+VEG+V T H++YA 
Sbjct: 72  SPPPSIPQERIERALREDKLDELLETVVELHQQAADDENIEQDIVVVEGLVSTEHSTYAN 131

Query: 119 RVNFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRG--- 175
           ++N HLA +LDA +I V   +     EL ++++I A+ FGG    + LG IL +++    
Sbjct: 132 QLNAHLAHALDARIIFVGTGDYHAPRELAEQLDIHARSFGGLASARTLGCILMRMKHLPN 191

Query: 176 ---------EADAANAEDGVADFARRLTEHSPLLRDD-FRLIGCIPWQDELNAARTRDIA 225
                     A +A  +D +    RR   ++P L  D F +IG +P+ D L+  R RD+A
Sbjct: 192 ATSEIPIAPGAGSAPLDDALVTELRR---YAPALATDRFHMIGVVPFSDTLSVPRIRDVA 248

Query: 226 DLLSARVINAGDYEQRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMN 285
             + A+ +N GD + RRV    LC R   + + + KPG L+VT GDRDDI+LAA+L  MN
Sbjct: 249 AAVGAKWLNEGDADSRRVLATSLCGRRAAHALDVFKPGSLIVTSGDRDDILLAAALVTMN 308

Query: 286 GVPLAGLLLCSDFPPDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRE 345
           G PLAG++L + + P+  +++ C  AL+ GLPV++V T S++T  +L+RM+ EIPVDD E
Sbjct: 309 GTPLAGVMLTNGYLPNQAMIDACTPALKTGLPVMAVETNSFNTVQDLSRMSNEIPVDDLE 368

Query: 346 RAERVTEFVAGHIDFEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRT 405
           RA++V  FVAGHID +WLK         RLSP AFR+Q+VQ+AQ+A KRIVLPEG+EPRT
Sbjct: 369 RADQVARFVAGHIDLQWLKDHLSRGYPRRLSPSAFRHQLVQKAQQAKKRIVLPEGNEPRT 428

Query: 406 VQAAAICQARGIARCVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRK 465
           ++AAA+CQ RG+A CVLLAK EEV+ VA+ +GI LP  LEIIDPD +   YV  MVE R+
Sbjct: 429 IEAAALCQRRGLAHCVLLAKREEVENVARTRGIDLPADLEIIDPDSIYMNYVAAMVERRR 488

Query: 466 GKGLNAPMAEQQLEDSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLV 525
           GK LN PMAE QL+D+VVL TMML   +VDGLVSGA+HTTA+T+RPA QLIKTAP Y LV
Sbjct: 489 GK-LNEPMAEAQLQDTVVLGTMMLYQGDVDGLVSGAVHTTANTVRPAFQLIKTAPDYRLV 547

Query: 526 SSVFFMLLPDQVLVYGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSG 585
           SS+FFMLLP+QV+VYGDCAVNPDP+  +LAEIA+QSA SA AFGI A+VAMISYSTG+SG
Sbjct: 548 SSIFFMLLPEQVVVYGDCAVNPDPNPEELAEIAIQSARSAIAFGIEAKVAMISYSTGESG 607

Query: 586 SGVDVDKVREATRLAREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDL 645
           SG DVDKVREATR+ARE+ P+LLIDGPLQYDAAAI SVGRQKAP+SPVAGQATVF+FPDL
Sbjct: 608 SGSDVDKVREATRIARERAPELLIDGPLQYDAAAIDSVGRQKAPDSPVAGQATVFVFPDL 667

Query: 646 NTGNTTYKAVQRSADCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           NTGNTTYKAVQRSA  VSVGPMLQGL KPVNDLSRGALV+DIVYTIALTAIQA
Sbjct: 668 NTGNTTYKAVQRSAKVVSVGPMLQGLNKPVNDLSRGALVDDIVYTIALTAIQA 720


Lambda     K      H
   0.319    0.136    0.388 

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: 1343
Number of extensions: 62
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: 704
Length of database: 727
Length adjustment: 39
Effective length of query: 665
Effective length of database: 688
Effective search space:   457520
Effective search space used:   457520
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: 55 (25.8 bits)

Align candidate WP_043530028.1 JH15_RS10540 (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.2174619.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.8e-126  405.8   0.0     1e-125  405.2   0.0    1.3  1  NCBI__GCF_000759345.1:WP_043530028.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000759345.1:WP_043530028.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.2   0.0    1e-125    1e-125       1     304 []     418     717 ..     418     717 .. 0.97

  Alignments for each domain:
  == domain 1  score: 405.2 bits;  conditional E-value: 1e-125
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           ivlPEg+e+r+++Aaal++++++a++vll++ ee++++ ++++++l +  ++++dpd+     +yv +++e+r
  NCBI__GCF_000759345.1:WP_043530028.1 418 IVLPEGNEPRTIEAAALCQRRGLAHCVLLAKREEVENVaRTRGIDLPAD-LEIIDPDSI--YMNYVAAMVERR 487
                                           8******************************999999867888888765.555666665..589********* PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           + k ++e +a+ ql+D+v+l+++++++g +dglvsGav+tta+t+rpa+q+ikt++  +lvss+f+m ++e+v
  NCBI__GCF_000759345.1:WP_043530028.1 488 RGK-LNEPMAEAQLQDTVVLGTMMLYQGDVDGLVSGAVHTTANTVRPAFQLIKTAPDYRLVSSIFFMLLPEQV 559
                                           ***.********************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                           +v++DCav++dPn+eeLAeiA+qsa sa ++g +e kva++syst+ sg+g++v+kv+eA++i++e++p+ll+
  NCBI__GCF_000759345.1:WP_043530028.1 560 VVYGDCAVNPDPNPEELAEIAIQSARSAIAFG-IEAKVAMISYSTGESGSGSDVDKVREATRIARERAPELLI 631
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           dG+lq+DaA +++v ++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+a++ ++GP+lqGl+kPvnDLsRGa
  NCBI__GCF_000759345.1:WP_043530028.1 632 DGPLQYDAAAIDSVGRQKAPDSPVAGQATVFVFPDLNTGNTTYKAVQRSAKVVSVGPMLQGLNKPVNDLSRGA 704
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v+div+++++ta
  NCBI__GCF_000759345.1:WP_043530028.1 705 LVDDIVYTIALTA 717
                                           ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (727 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: 35.08
//
[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