Alignments for a candidate for pta in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Pseudomonas benzenivorans DSM 8628

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_090447850.1 BLS63_RS21525 phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>NCBI__GCF_900100495.1:WP_090447850.1
          Length = 697

 Score = 1166 bits (3017), Expect = 0.0
 Identities = 594/699 (84%), Positives = 644/699 (92%), Gaps = 8/699 (1%)

Query: 1   MHTFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTH 60
           MHTFFI+PTGFGVGLTSISLGL+ ALERAGLKVGFFKPIAQ H GD GPERSSEL+ARTH
Sbjct: 1   MHTFFISPTGFGVGLTSISLGLVGALERAGLKVGFFKPIAQPHQGDAGPERSSELIARTH 60

Query: 61  GLDTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAARV 120
           GL +PKPL LA VERMLGDGQLDELLEEIISLYQ+AAA KDVVIVEGMVPTR ASYAARV
Sbjct: 61  GLHSPKPLALAHVERMLGDGQLDELLEEIISLYQQAAAGKDVVIVEGMVPTRQASYAARV 120

Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAA 180
           NFHLAKSLDA+VILVSAPE E+L EL DR+EIQAQLFGGP+DPKVLGVI+NKVR      
Sbjct: 121 NFHLAKSLDADVILVSAPEQESLAELCDRVEIQAQLFGGPKDPKVLGVIINKVR------ 174

Query: 181 NAEDGVADFARRLTEHSPLLR-DDFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYE 239
            +EDG   F  RL EHSPLLR DDFRL+GCIPWQDELNA RTRDIADLL ARV+NAGDYE
Sbjct: 175 -SEDGFEAFCERLKEHSPLLRSDDFRLLGCIPWQDELNAPRTRDIADLLGARVLNAGDYE 233

Query: 240 QRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFP 299
           QRR+ KI+LCARAV NTVQLLKPG LVVTPGDRDDIILAASLAAMNG+PLAGLLLCSDF 
Sbjct: 234 QRRILKIMLCARAVANTVQLLKPGTLVVTPGDRDDIILAASLAAMNGMPLAGLLLCSDFV 293

Query: 300 PDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHID 359
           PDPRIMELCRGALQ GLPV++V+TGSYDTAT+LNR+NKEIPVDD+ERAE+V +FVA HID
Sbjct: 294 PDPRIMELCRGALQSGLPVMTVSTGSYDTATDLNRLNKEIPVDDKERAEKVADFVASHID 353

Query: 360 FEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIAR 419
            +WL+ RCGTPRELRLSP AFRYQ+VQRA+ A KRIVLPEGSEPRTV+AAAICQARGIAR
Sbjct: 354 HDWLRARCGTPRELRLSPSAFRYQLVQRAKAADKRIVLPEGSEPRTVKAAAICQARGIAR 413

Query: 420 CVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLE 479
           CVLLAKP+EV+AVA+AQGI LP GLEI+DPDL+R+RYVEPM+ELRKGKGLNAPMA  QLE
Sbjct: 414 CVLLAKPDEVRAVARAQGIELPPGLEILDPDLIRERYVEPMIELRKGKGLNAPMAFAQLE 473

Query: 480 DSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 539
           D+VVL TMMLALDEVDGLVSGA+HTTA+TIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV
Sbjct: 474 DNVVLGTMMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLV 533

Query: 540 YGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRL 599
           YGDCAVNPDPSA+ LAEIA+QSAASA AFGIP RVAM+SYSTGDSG+G +V+KVREATRL
Sbjct: 534 YGDCAVNPDPSAAQLAEIALQSAASASAFGIPPRVAMLSYSTGDSGTGEEVEKVREATRL 593

Query: 600 AREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSA 659
           AR+  P L +DGPLQYDAA I SVGRQKAPNSPVAG+ATVF+FPDLNTGNTTYKAVQRSA
Sbjct: 594 ARQLDPQLALDGPLQYDAATIDSVGRQKAPNSPVAGRATVFVFPDLNTGNTTYKAVQRSA 653

Query: 660 DCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           DCVSVGPMLQGLRKPVNDLSRGALV+DIVYTIALTAIQA
Sbjct: 654 DCVSVGPMLQGLRKPVNDLSRGALVDDIVYTIALTAIQA 692


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: 1464
Number of extensions: 53
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: 697
Length adjustment: 39
Effective length of query: 665
Effective length of database: 658
Effective search space:   437570
Effective search space used:   437570
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: 54 (25.4 bits)

Align candidate WP_090447850.1 BLS63_RS21525 (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.31086.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.1e-128  412.1   0.0   1.2e-127  411.5   0.0    1.3  1  lcl|NCBI__GCF_900100495.1:WP_090447850.1  BLS63_RS21525 phosphate acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090447850.1  BLS63_RS21525 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.5   0.0  1.2e-127  1.2e-127       1     304 []     389     689 ..     389     689 .. 0.98

  Alignments for each domain:
  == domain 1  score: 411.5 bits;  conditional E-value: 1.2e-127
                                 TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverl 68 
                                               ivlPEgse+r++kAaa+++ ++ia++vll++ +e+ ++ +a++++l  g +++ dpd+   +e+yve +
  lcl|NCBI__GCF_900100495.1:WP_090447850.1 389 IVLPEGSEPRTVKAAAICQARGIARCVLLAKPDEVRAVaRAQGIELPPG-LEILDPDLI--RERYVEPM 454
                                               8**********************************99978999999876.678889999..8******* PP

                                 TIGR00651  69 yekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvf 137
                                               +e+rk kG++  +a  ql+D+v+l++++++l+e+dglvsGav+tta+t+rpalq+ikt++g +lvssvf
  lcl|NCBI__GCF_900100495.1:WP_090447850.1 455 IELRKGKGLNAPMAFAQLEDNVVLGTMMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGYNLVSSVF 523
                                               ********************************************************************* PP

                                 TIGR00651 138 imekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAv 206
                                               +m ++++vlv++DCav++dP+a +LAeiAlqsa+sa ++g + p+va+lsyst+ sg geevekv+eA+
  lcl|NCBI__GCF_900100495.1:WP_090447850.1 524 FMLLPDQVLVYGDCAVNPDPSAAQLAEIALQSAASASAFG-IPPRVAMLSYSTGDSGTGEEVEKVREAT 591
                                               ****************************************.**************************** PP

                                 TIGR00651 207 kilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGP 275
                                               +++++  p+l+ldG+lq+DaA +++v ++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+ad  ++GP
  lcl|NCBI__GCF_900100495.1:WP_090447850.1 592 RLARQLDPQLALDGPLQYDAATIDSVGRQKAPNSPVAGRATVFVFPDLNTGNTTYKAVQRSADCVSVGP 660
                                               ********************************************************************* PP

                                 TIGR00651 276 ilqGlakPvnDLsRGasvedivnvviita 304
                                               +lqGl+kPvnDLsRGa+v+div+++++ta
  lcl|NCBI__GCF_900100495.1:WP_090447850.1 661 MLQGLRKPVNDLSRGALVDDIVYTIALTA 689
                                               ***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (697 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: 19.06
//
[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:

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