Alignments for a candidate for pta in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Pseudomonas stutzeri RCH2

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate GFF3155 Psest_3214 phosphate acetyltransferase

Query= BRENDA::C1DQG8
         (712 letters)



>FitnessBrowser__psRCH2:GFF3155
          Length = 698

 Score = 1134 bits (2933), Expect = 0.0
 Identities = 580/695 (83%), Positives = 639/695 (91%), Gaps = 1/695 (0%)

Query: 1   MHTLFLAPTGYAVGLNSISLGLIRALEQAGLKVGFFKPIAQPFPIDQGRERSCLLVERTL 60
           MHT+FLAPTG+  GLNSISLGLIRALE AGLKVGFFKPIAQPFP+DQGRERSC+LVERTL
Sbjct: 1   MHTIFLAPTGFGGGLNSISLGLIRALENAGLKVGFFKPIAQPFPVDQGRERSCILVERTL 60

Query: 61  GRSTPEPILLDQVERHLASGETDLLLEEVVSRYQQAAAGKDVVIVEGMLPTRDSDYSAYL 120
             ++PEP+ L+QVER LA GE DLLLE+VVSRYQQ AAGKDVVIVEGM+PTR+S+Y+  +
Sbjct: 61  KLTSPEPLPLEQVERQLADGEIDLLLEDVVSRYQQVAAGKDVVIVEGMVPTRESNYTQRI 120

Query: 121 NPLLSKSLNAEVILIAVQGGDGLKQLAERIEIQAQLFGGIKSPKVLGAIINKIDSGDGIP 180
           N  L+KSL+AEVILIA QG D LK+LAERIEIQAQL+GG K PKVLG I+NK+ + +G+P
Sbjct: 121 NTQLAKSLDAEVILIAAQGNDSLKRLAERIEIQAQLYGGAKDPKVLGVILNKVKTEEGLP 180

Query: 181 AFVERLKEYLPSLGSTDFQLFGAIPFAEELNALRTRDVAELIGAQVLSAGEADRRRVSKI 240
           AF++ LK++LP LGS DFQL GAIPF+EELNALRTRD+AEL+GAQVL+AGEAD+RRV+KI
Sbjct: 181 AFIDSLKQHLPLLGSADFQLLGAIPFSEELNALRTRDIAELLGAQVLNAGEADQRRVNKI 240

Query: 241 VLCARAVPSTVPLLQPGVLVVTPGDRDDVILAASLASLNGVKLAGLLLCSDFMPDPRIME 300
           VLCARAVP+TV LLQ GVLVVTPGDRDD+ILAASLASLNG KLAGLLLCSDF PDPRI+E
Sbjct: 241 VLCARAVPNTVQLLQSGVLVVTPGDRDDIILAASLASLNGEKLAGLLLCSDFAPDPRILE 300

Query: 301 LCKAALDGGLPVMSVTTGSYDTATNLFALNKETPADDIERATRVTDFIAGHLHPEYLRSR 360
           LCKAALDGGLPVM+V T SYDTA NLF LNKETPADDIERATRVTDFIA HLHPE+L +R
Sbjct: 301 LCKAALDGGLPVMTVETNSYDTANNLFGLNKETPADDIERATRVTDFIAKHLHPEFLHTR 360

Query: 361 CSLPR-ELLLSPPAFRYQLVKSAQEADKRIVLPEGTEPRTIRAAAICQERGIARCVLLAR 419
           CS+PR EL +SP AFRYQLVK AQ+A+KRIVLPEG EPRTIRAAAICQERGIARCVLLA+
Sbjct: 361 CSVPRGELRMSPAAFRYQLVKRAQDANKRIVLPEGNEPRTIRAAAICQERGIARCVLLAK 420

Query: 420 PEEVRAVAREQGITLPDGLEILDPESIRAQYIAPMVKMRQSKGLTPEMADEQLRDTVVLG 479
           PEEV+ VAREQGI+LP  LEILDP+SI  +Y+ PM +MR++KGLTPE A EQL+DTVVLG
Sbjct: 421 PEEVQQVAREQGISLPASLEILDPDSIANRYVEPMCEMRKAKGLTPEDAREQLKDTVVLG 480

Query: 480 TMMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLVYGDCAV 539
           TMMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGY+LVSSVFFMLLPDQVLVYGDCAV
Sbjct: 481 TMMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGYSLVSSVFFMLLPDQVLVYGDCAV 540

Query: 540 NPNPSAAELAEIALQSAESAVALGVHPRVAMISYSTGDSGSGAEVDKVREATRIAQERAP 599
           NPNPSA ELAEIALQSAESAVALGV+PRVAMISYSTG SGSGAEV+KV EATRIAQERAP
Sbjct: 541 NPNPSATELAEIALQSAESAVALGVNPRVAMISYSTGSSGSGAEVEKVAEATRIAQERAP 600

Query: 600 GLPIDGPLQYDAASVASVGKQKAPNSPVAGQATVFVFPDLNTGNTTYKAVQRNANCISVG 659
            LPIDGPLQYDAASV SVGKQKAPNS VAGQATVF+FPDLNTGNTTYKAVQRNANC+SVG
Sbjct: 601 ALPIDGPLQYDAASVLSVGKQKAPNSKVAGQATVFIFPDLNTGNTTYKAVQRNANCLSVG 660

Query: 660 PMLQGLAKPVNDLSRGALVDDIVFTIALTALQAAS 694
           PMLQGLAKPVNDLSRGALVDDIVFTIALTALQAA+
Sbjct: 661 PMLQGLAKPVNDLSRGALVDDIVFTIALTALQAAN 695


Lambda     K      H
   0.318    0.135    0.379 

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: 1522
Number of extensions: 68
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: 712
Length of database: 698
Length adjustment: 39
Effective length of query: 673
Effective length of database: 659
Effective search space:   443507
Effective search space used:   443507
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: 54 (25.4 bits)

Align candidate GFF3155 Psest_3214 (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.9332.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.5e-129  417.8   0.1   2.2e-129  417.2   0.1    1.3  1  lcl|FitnessBrowser__psRCH2:GFF3155  Psest_3214 phosphate acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3155  Psest_3214 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.2   0.1  2.2e-129  2.2e-129       1     304 []     390     690 ..     390     690 .. 0.97

  Alignments for each domain:
  == domain 1  score: 417.2 bits;  conditional E-value: 2.2e-129
                           TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekrkh 74 
                                         ivlPEg+e+r+++Aaa+++e++ia++vll++ ee++++ + +++ l ++ +++ dpd+    ++yve + e rk+
  lcl|FitnessBrowser__psRCH2:GFF3155 390 IVLPEGNEPRTIRAAAICQERGIARCVLLAKPEEVQQVaREQGISLPAS-LEILDPDSI--ANRYVEPMCEMRKA 461
                                         8************************************866777777655.667777777..69************ PP

                           TIGR00651  75 kGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevlvfa 149
                                         kG+t + areql+D+v+l++++++l+e+dglvsGav+tta+t+rpalq+ikt++g +lvssvf+m ++++vlv++
  lcl|FitnessBrowser__psRCH2:GFF3155 462 KGLTPEDAREQLKDTVVLGTMMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGYSLVSSVFFMLLPDQVLVYG 536
                                         *************************************************************************** PP

                           TIGR00651 150 DCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllldGelqf 224
                                         DCav+++P+a eLAeiAlqsa+sa +lg  +p+va++syst++sg+g+evekv+eA++i++e++p l +dG+lq+
  lcl|FitnessBrowser__psRCH2:GFF3155 537 DCAVNPNPSATELAEIALQSAESAVALG-VNPRVAMISYSTGSSGSGAEVEKVAEATRIAQERAPALPIDGPLQY 610
                                         ****************************.********************************************** PP

                           TIGR00651 225 DaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGasvedivnv 299
                                         DaA v +v ++kap+s+vag+a+vf+FPdL++Gn++Yk+vqR a+  ++GP+lqGlakPvnDLsRGa+v+div++
  lcl|FitnessBrowser__psRCH2:GFF3155 611 DAASVLSVGKQKAPNSKVAGQATVFIFPDLNTGNTTYKAVQRNANCLSVGPMLQGLAKPVNDLSRGALVDDIVFT 685
                                         *************************************************************************** PP

                           TIGR00651 300 viita 304
                                         +++ta
  lcl|FitnessBrowser__psRCH2:GFF3155 686 IALTA 690
                                         ***96 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 13.85
//
[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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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