Alignments for a candidate for pta in Psychrobacter cryohalolentis K5

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Psychrobacter cryohalolentis K5

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_011512589.1 PCRYO_RS01130 phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>NCBI__GCF_000013905.1:WP_011512589.1
          Length = 718

 Score =  735 bits (1897), Expect = 0.0
 Identities = 394/717 (54%), Positives = 501/717 (69%), Gaps = 23/717 (3%)

Query: 1   MHTFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDL--GPERSSELVAR 58
           M T  + P   G+G+TS +LGL+RA +  G+K GF KP  Q    D     + SS L   
Sbjct: 1   MQTILLVPISRGIGVTSAALGLIRAFDYNGIKAGFMKPFLQDDTLDKQNSLDSSSALAMH 60

Query: 59  THGLDTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAA 118
             GL  PK +    VERM+GD  LD+L+EE++  Y     D DVVI EG+VPT   SYA+
Sbjct: 61  AFGLKPPKSISRQHVERMIGDDNLDDLMEEVVVNYHTLGDDYDVVICEGLVPTTETSYAS 120

Query: 119 RVNFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVR---- 174
           ++N  +A +LDA +I VS  +      L D++++ A+ FGG    + LG IL ++     
Sbjct: 121 QINRAIAHALDARIIFVSTADTSKPAYLADKLDVHAREFGGMASDRTLGCILMRMHDLPN 180

Query: 175 ------------GEADAANAEDGVADFARRLTEHSPLLRDDFRLIGCIPWQDELNAARTR 222
                       GEA   + + G     +RL+ H     + FRLIG +P+ D L+  RT 
Sbjct: 181 TQSTLENQIVAPGEA-IVSLDSGFIQEVQRLSPH--FNTEQFRLIGVVPFSDSLSVPRTW 237

Query: 223 DIADLLSARVINAGDYEQRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLA 282
           DIA  L    +N G+ + RR+ +I L AR+V    ++ K G L+V PGDRDD++LAA LA
Sbjct: 238 DIAAELDGTWLNVGEAKSRRINRISLTARSVARVDEVFKRGTLIVVPGDRDDLLLAAGLA 297

Query: 283 AMNGVPLAGLLLCSDFPPDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVD 342
            +NG+PLAGL+L     P P + EL + AL+ G+PV+SV   S++T  +L  M+ EIP D
Sbjct: 298 CINGIPLAGLVLTGGVVPSPTVAELWQSALKTGIPVMSVEDDSFETVQSLLHMSAEIPSD 357

Query: 343 DRERAERVTEFVAGHIDFEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSE 402
           D ERAE V  +VA H+D  W+K       E RLSP AFR+QVV++AQ A KRIVLPEGSE
Sbjct: 358 DTERAEEVARYVAAHLDLSWIKAYFSQNHEPRLSPSAFRHQVVKKAQIAKKRIVLPEGSE 417

Query: 403 PRTVQAAAICQARGIARCVLLAKPEEVQAVAQAQGIVLPEGLEIIDPD-LVRQRYVEPMV 461
           PRTV+AA ICQ+RGIA CVLLAK  +V+ VA+ + +VLPEGLEIIDPD L   +Y+  +V
Sbjct: 418 PRTVEAACICQSRGIANCVLLAKRADVEQVAKNRDLVLPEGLEIIDPDSLDMSKYIAAVV 477

Query: 462 ELRKGKGLNAPMAEQQLEDSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPG 521
           E RKGK  +A +A + L+D+V L T ML +DEVDGLVSGAIHTTA+T+RPA QLIKTAP 
Sbjct: 478 ERRKGK-TSAEVAAEYLQDTVYLGTTMLQMDEVDGLVSGAIHTTANTVRPAFQLIKTAPE 536

Query: 522 YNLVSSVFFMLLPDQVLVYGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYST 581
           Y+LVSSVFFMLLP+QV+VYGDCA+NPDP+A +LAEIA+QSA SA AFGI  +VAMISYST
Sbjct: 537 YSLVSSVFFMLLPEQVVVYGDCAINPDPNAEELAEIAIQSAQSAAAFGIDPKVAMISYST 596

Query: 582 GDSGSGVDVDKVREATRLAREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFI 641
           G SG+G DV+KV  AT++ RE+ P+L +DGPLQYDAA++ SVG+QKAP+SPVAGQA VFI
Sbjct: 597 GSSGTGADVEKVARATQIVRERAPNLKVDGPLQYDAASVMSVGKQKAPDSPVAGQANVFI 656

Query: 642 FPDLNTGNTTYKAVQRSADCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           FPDLNTGNTTYKAVQRSA+ VSVGPMLQGL KPVNDLSRGALV+DI+YTIALTAIQA
Sbjct: 657 FPDLNTGNTTYKAVQRSANVVSVGPMLQGLNKPVNDLSRGALVDDIIYTIALTAIQA 713


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: 1205
Number of extensions: 44
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: 718
Length adjustment: 39
Effective length of query: 665
Effective length of database: 679
Effective search space:   451535
Effective search space used:   451535
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_011512589.1 PCRYO_RS01130 (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.3411783.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-127  410.7   0.6   2.9e-127  410.3   0.6    1.2  1  NCBI__GCF_000013905.1:WP_011512589.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013905.1:WP_011512589.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.3   0.6  2.9e-127  2.9e-127       1     304 []     410     710 ..     410     710 .. 0.97

  Alignments for each domain:
  == domain 1  score: 410.3 bits;  conditional E-value: 2.9e-127
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlkl.gkvvvedpdvskdiekyverlyekr 72 
                                           ivlPEgse+r+++Aa ++++++ia++vll++ +++++  ak+ +l l + ++++dpd+  d+ ky+ +++e+r
  NCBI__GCF_000013905.1:WP_011512589.1 410 IVLPEGSEPRTVEAACICQSRGIANCVLLAKRADVEQ-VAKNRDLVLpEGLEIIDPDSL-DMSKYIAAVVERR 480
                                           8******************************999999.566666665256899****99.9************ PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           k k  + + a+e l+D+v+l++++++++e+dglvsGa +tta+t+rpa+q+ikt++  +lvssvf+m ++e+v
  NCBI__GCF_000013905.1:WP_011512589.1 481 KGK-TSAEVAAEYLQDTVYLGTTMLQMDEVDGLVSGAIHTTANTVRPAFQLIKTAPEYSLVSSVFFMLLPEQV 552
                                           ***.89999**************************************************************** PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                           +v++DCa+++dPnaeeLAeiA+qsa+sa ++g ++pkva++syst++sg g++vekv+ A++i++e++p+l++
  NCBI__GCF_000013905.1:WP_011512589.1 553 VVYGDCAINPDPNAEELAEIAIQSAQSAAAFG-IDPKVAMISYSTGSSGTGADVEKVARATQIVRERAPNLKV 624
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           dG+lq+DaA v +v ++kap+s+vag+anvf+FPdL++Gn++Yk+vqR+a++ ++GP+lqGl+kPvnDLsRGa
  NCBI__GCF_000013905.1:WP_011512589.1 625 DGPLQYDAASVMSVGKQKAPDSPVAGQANVFIFPDLNTGNTTYKAVQRSANVVSVGPMLQGLNKPVNDLSRGA 697
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v+di++++++ta
  NCBI__GCF_000013905.1:WP_011512589.1 698 LVDDIIYTIALTA 710
                                           ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (718 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 44.20
//
[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