GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Marinobacter adhaerens HP15

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate GFF1534 HP15_1498 phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>FitnessBrowser__Marino:GFF1534
          Length = 709

 Score =  763 bits (1970), Expect = 0.0
 Identities = 405/699 (57%), Positives = 505/699 (72%), Gaps = 18/699 (2%)

Query: 14  GLTSISLGLLRALERAGLKVGFFKPIAQ-LHPGD----LGPERSSELVARTHGLDTPKPL 68
           GLTS+ LGLLRALER G+ VGF+KP  Q +H  +     G + S   V  +  L+ P P+
Sbjct: 4   GLTSVCLGLLRALERVGVSVGFYKPFCQAVHRAESMHNAGQDSSVAFVRASSHLNPPDPI 63

Query: 69  PLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAARVNFHLAKSL 128
            L + +++L  G+ D LLE ++  YQ+ A D DVVI+EG+VP R  +Y AR+N  +A++L
Sbjct: 64  ALKEAQQLLNRGKADYLLETVVGEYQKVARDVDVVIIEGLVPDRSEAYIARLNVEVARNL 123

Query: 129 DAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAANAEDG--- 185
            +EVILVS P++    +L + ++  ++LF  P DP V+GVILNKV GE + +  E     
Sbjct: 124 GSEVILVSTPKDLDARQLDEELDFSSRLFASPSDPDVIGVILNKV-GEPEQSGLEPRSNN 182

Query: 186 ------VADFARRLTEHSPLLRDDFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYE 239
                   D+    T  S      F L+  IPWQ +L A R  DIA  L   V+N G   
Sbjct: 183 NHPAPVTVDYQTECTVFS---EGRFHLLAEIPWQADLLAPRVSDIARELGLPVLNEGQMH 239

Query: 240 QRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFP 299
            RRVQK+ +CAR++ N  + L+PG L+VTPGDR+DI++A ++AA+NGVPLAGL+L     
Sbjct: 240 ARRVQKVSVCARSIRNMTETLRPGTLLVTPGDREDIVVATAVAALNGVPLAGLMLTGGLI 299

Query: 300 PDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHID 359
           PD R++ LC  AL+ GLPVL     +Y+TA  L  ++  IP+DD  R E+  E VA  ID
Sbjct: 300 PDQRVITLCHRALETGLPVLGSDANTYETAHMLANLSAAIPIDDPNRIEKAMEAVATRID 359

Query: 360 FEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIAR 419
             WL+Q     R+ RLSPPAFRYQ+ +RA+ A KRI+LPEGSEPRTVQAA IC  R +AR
Sbjct: 360 TNWLQQHLKVARQDRLSPPAFRYQLSERARAANKRIILPEGSEPRTVQAAIICHQRRLAR 419

Query: 420 CVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLE 479
           C L+    E++ VA +Q + LP  +EIIDP  VRQRYV PMVELRK KGL + MAE  LE
Sbjct: 420 CALIGNAAEIKRVADSQDLELPGDIEIIDPGEVRQRYVAPMVELRKHKGLTSDMAEAMLE 479

Query: 480 DSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 539
           D+VVL TMM+ALDE DGLVSGAIHTTA+T+RPALQLIKT     +VSSVFFMLLP QV+V
Sbjct: 480 DNVVLGTMMVALDEADGLVSGAIHTTANTVRPALQLIKTHEHAKVVSSVFFMLLPQQVVV 539

Query: 540 YGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRL 599
           YGDCA+NPDP+A +LA+IA+QSA SA+AFGI   VAMISYSTG+SGSG DV+KVREATR+
Sbjct: 540 YGDCAINPDPNAEELADIAIQSAESAEAFGIEPLVAMISYSTGESGSGQDVEKVREATRI 599

Query: 600 AREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSA 659
           ARE+RPDLLIDGPLQYDAAAI SV R KAP+S VAG+ATVF+FPDLNTGNTTYKAVQRSA
Sbjct: 600 ARERRPDLLIDGPLQYDAAAIESVARSKAPDSKVAGKATVFVFPDLNTGNTTYKAVQRSA 659

Query: 660 DCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           + VSVGPMLQGLRKPVNDLSRGALVEDIV+T+ALTA+QA
Sbjct: 660 NVVSVGPMLQGLRKPVNDLSRGALVEDIVFTVALTAVQA 698


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: 1258
Number of extensions: 46
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: 704
Length of database: 709
Length adjustment: 39
Effective length of query: 665
Effective length of database: 670
Effective search space:   445550
Effective search space used:   445550
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 GFF1534 HP15_1498 (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.11245.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.2e-131  424.7   0.2   1.7e-131  424.2   0.2    1.2  1  lcl|FitnessBrowser__Marino:GFF1534  HP15_1498 phosphate acetyltransf


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF1534  HP15_1498 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  424.2   0.2  1.7e-131  1.7e-131       1     304 []     395     695 ..     395     695 .. 0.97

  Alignments for each domain:
  == domain 1  score: 424.2 bits;  conditional E-value: 1.7e-131
                           TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkh 74 
                                         i+lPEgse+r+++Aa+++ ++++a+++l++n +e++++  +++++l  g+++++dp     +++yv  ++e+rkh
  lcl|FitnessBrowser__Marino:GFF1534 395 IILPEGSEPRTVQAAIICHQRRLARCALIGNAAEIKRVaDSQDLELP-GDIEIIDPGEV--RQRYVAPMVELRKH 466
                                         8************************************7556666665.66667776666..69************ PP

                           TIGR00651  75 kGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfa 149
                                         kG+t  +a+ +l+D+v+l++++v+l+eadglvsGa +tta+t+rpalq+ikt+e  k+vssvf+m ++++v+v++
  lcl|FitnessBrowser__Marino:GFF1534 467 KGLTSDMAEAMLEDNVVLGTMMVALDEADGLVSGAIHTTANTVRPALQLIKTHEHAKVVSSVFFMLLPQQVVVYG 541
                                         *************************************************************************** PP

                           TIGR00651 150 DCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqf 224
                                         DCa+++dPnaeeLA+iA+qsa+sa+++g +ep va++syst+ sg+g++vekv+eA++i++e++pdll+dG+lq+
  lcl|FitnessBrowser__Marino:GFF1534 542 DCAINPDPNAEELADIAIQSAESAEAFG-IEPLVAMISYSTGESGSGQDVEKVREATRIARERRPDLLIDGPLQY 615
                                         ****************************.********************************************** PP

                           TIGR00651 225 DaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnv 299
                                         DaA +e+va++kap+s+vagka+vfvFPdL++Gn++Yk+vqR+a++ ++GP+lqGl+kPvnDLsRGa+vediv++
  lcl|FitnessBrowser__Marino:GFF1534 616 DAAAIESVARSKAPDSKVAGKATVFVFPDLNTGNTTYKAVQRSANVVSVGPMLQGLRKPVNDLSRGALVEDIVFT 690
                                         *************************************************************************** PP

                           TIGR00651 300 viita 304
                                         v++ta
  lcl|FitnessBrowser__Marino:GFF1534 691 VALTA 695
                                         ***96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (709 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: 00:00:00.01
# Mc/sec: 18.96
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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