Alignments for a candidate for pta in Gallaecimonas xiamenensis 3-C-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Gallaecimonas xiamenensis 3-C-1

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_008485467.1 B3C1_RS13430 phosphate acetyltransferase

Query= BRENDA::C1DER7
         (691 letters)



>NCBI__GCF_000299915.1:WP_008485467.1
          Length = 676

 Score =  564 bits (1453), Expect = e-165
 Identities = 337/694 (48%), Positives = 425/694 (61%), Gaps = 31/694 (4%)

Query: 2   QTFLIAPSSYGVGLTSISLGLVRALERYGLKVGFFKPVAQPHPGDCGPERTSALIARTHH 61
           +T L+ P   G  LT++SLGLV AL+R GL +GF KP++     D   +RT A++     
Sbjct: 3   KTLLLVPVGTGAALTAVSLGLVHALQRQGLDLGFSKPISPA--ADPAADRTIAVLNSVVP 60

Query: 62  LDPPEPLPLARVERRLGDGQLNELLEDIVGRLQQLENGHDVLIVEGLVPSPQVGYAARLN 121
              P PL LA V + L        L     RL     G+ + +V G+   P       LN
Sbjct: 61  GVLPCPLALA-VAKDLDPADFEAAL---FSRLP----GNQLCVVAGVPHEPA------LN 106

Query: 122 GHLARSLNADVILVSTPAEESLEELRDHLEIQARLLGAGQDTPVAGAILN-KVPPGPLAE 180
             LA+ LNA VIL++     S ++L   L      LG G    V G ILN K+ P  L  
Sbjct: 107 ILLAQRLNAKVILLAARDGTSTQQLAQVLAQCEAALGQGS---VEGLILNHKLSPRTLGR 163

Query: 181 RLCQP-------EPLGRNLRLLGCVPWRDTLNTPRTSDIADLLGARLLNPGDYRQRRVQH 233
               P       E L   LRLL  +PWR  L  PR  D+A  L A  L  GD++ RR+ H
Sbjct: 164 SALGPGQGPDTLEALPAALRLLADIPWRGDLIAPRVWDLAQHLNALPLCSGDWQSRRLNH 223

Query: 234 SLLCAAAAPSLLPRFKPGTLLLAPGDRHDVILAAGLASRNGMSLAGLLLCGALPADERVL 293
            L         + +   GTL++ PGD  DVI+A  LA++NG+ L GLLL G +     ++
Sbjct: 224 LLTPTQPLQEWVGKLCHGTLVVTPGDSSDVIVATCLAAQNGVRLGGLLLTGGIQPQPAIM 283

Query: 294 ELCRPAMADGLPVLAVERDPEDTLRELERLNREIPLDDLERAERISDYVASHLDRAWFIQ 353
            LC  A   GLP+L V+ D   TL  +  L+  +P DD  R   I D VA HLD +W  Q
Sbjct: 284 ALCEDAFDAGLPLLMVDSDDSQTLAAIRELDLSLPADDDYRQRWIMDQVAEHLDSSWLSQ 343

Query: 354 RCGTPREPRLSPPAFRYNLVKRAQAANRRIVLPEGSEPRTVQAAAICQRRGIARCVLLAR 413
               P    LSPPAF Y L +RA+AA +RI+LPEG EPR ++AAA C  RGIA+CVLL +
Sbjct: 344 FIPPPASALLSPPAFAYQLQQRAKAAAKRIILPEGDEPRVIKAAAHCTERGIAQCVLLGK 403

Query: 414 PEEVQAVARAQGIELPAGLEIVDPEQIRERYVEPMVELRRHKGLSAPAARAQLEDNVVLG 473
           PE+VQAVAR  G+ LPA L I+DP+ +RERYV PMV LRR KGL    AR QL+DNVVL 
Sbjct: 404 PEQVQAVARHHGLTLPARLAIIDPDAVRERYVGPMVALRRQKGLEEVMAREQLQDNVVLA 463

Query: 474 TLMLALDEVDGLVSGAVHTTANTIRPALQLIKTAPGCKLVSSVFFMLLPEQVLVYGDCAV 533
           T+MLA  EVDGLVSGA  TT  T+RP +QLIKTAPG  +VSSVFFMLLP+QVL+YGDCA+
Sbjct: 464 TMMLAQGEVDGLVSGARGTTLQTLRPPMQLIKTAPGQSMVSSVFFMLLPDQVLIYGDCAI 523

Query: 534 NPDPSAEELADIALQSAASAQAFGIPPRVAMISYSTGASGEGADVEKVREATRLARQARP 593
           NP+P A +LA IALQ A SA+  GI P + MI+ + G +G      KV  A +L  + +P
Sbjct: 524 NPNPDAYQLAQIALQCADSAERLGIAPHITMIADNQGGTG----ASKVEHARQLLAELKP 579

Query: 594 DLPIDGPLQYDAAAIAEVARQKAPDSTVAGRATVFVFPDLNTGNTTYKAVQRSANCVSVG 653
           +L +DGPL YDAA I  VAR KAP S VAG+A +FVFPDLNTG +TY+AV+RSA+ V++G
Sbjct: 580 ELVVDGPLHYDAAVIESVARAKAPGSPVAGQANIFVFPDLNTGYSTYQAVRRSADLVTLG 639

Query: 654 PMLQGLRKPVNDLSRGALVDDIVFTIALTAIQAE 687
           PM+QG  KPVNDLSR A V D++ TIALTAIQAE
Sbjct: 640 PMVQGFAKPVNDLSRDAKVTDVIQTIALTAIQAE 673


Lambda     K      H
   0.319    0.137    0.398 

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: 1273
Number of extensions: 62
Number of successful extensions: 5
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: 691
Length of database: 676
Length adjustment: 39
Effective length of query: 652
Effective length of database: 637
Effective search space:   415324
Effective search space used:   415324
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_008485467.1 B3C1_RS13430 (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.2991865.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-106  342.6   0.0   1.5e-106  342.2   0.0    1.2  1  NCBI__GCF_000299915.1:WP_008485467.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000299915.1:WP_008485467.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  342.2   0.0  1.5e-106  1.5e-106       1     304 []     373     669 ..     373     669 .. 0.96

  Alignments for each domain:
  == domain 1  score: 342.2 bits;  conditional E-value: 1.5e-106
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           i+lPEg+e+rv+kAaa ++e++ia++vll++ e++++++ ++  +  +++ ++dpd    +e+yv  ++ +r+
  NCBI__GCF_000299915.1:WP_008485467.1 373 IILPEGDEPRVIKAAAHCTERGIAQCVLLGKPEQVQAVARHHGLTLPARLAIIDPDAV--RERYVGPMVALRR 443
                                           8***********************************9743333334467788888888..8************ PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                           +kG++e +areql+D+v+la++++++ge+dglvsGa  tt +tlrp++q+ikt++g ++vssvf+m ++++vl
  NCBI__GCF_000299915.1:WP_008485467.1 444 QKGLEEVMAREQLQDNVVLATMMLAQGEVDGLVSGARGTTLQTLRPPMQLIKTAPGQSMVSSVFFMLLPDQVL 516
                                           ************************************************************************* PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           +++DCa++++P+a +LA+iAlq a+sa+ lg + p++++++   +g g+     kv++A ++l e +p+l++d
  NCBI__GCF_000299915.1:WP_008485467.1 517 IYGDCAINPNPDAYQLAQIALQCADSAERLG-IAPHITMIADNQGGTGA----SKVEHARQLLAELKPELVVD 584
                                           *******************************.********999998886....589***************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           G+l +DaA++e+va+ kap s+vag+an+fvFPdL++G  +Y++v+R+ad+ ++GP++qG+akPvnDLsR a+
  NCBI__GCF_000299915.1:WP_008485467.1 585 GPLHYDAAVIESVARAKAPGSPVAGQANIFVFPDLNTGYSTYQAVRRSADLVTLGPMVQGFAKPVNDLSRDAK 657
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviita 304
                                           v d+++++++ta
  NCBI__GCF_000299915.1:WP_008485467.1 658 VTDVIQTIALTA 669
                                           **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (676 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 35.28
//
[ok]

This GapMind analysis is from Sep 24 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