Alignments for a candidate for pta in Marinobacter adhaerens HP15

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.2128.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 18.80
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources