Alignments for a candidate for pta in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Pedobacter sp. GW460-11-11-14-LB5

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate CA265_RS10075 CA265_RS10075 phosphate acetyltransferase

Query= metacyc::GIO2-991-MONOMER
         (792 letters)



>FitnessBrowser__Pedo557:CA265_RS10075
          Length = 695

 Score =  464 bits (1194), Expect = e-135
 Identities = 293/725 (40%), Positives = 427/725 (58%), Gaps = 53/725 (7%)

Query: 63  LFLSDISLVGQRTPLLLGFFNYFERHLPHVGFFEPIAAEALASSELRIDRHVELVYKVFN 122
           +F++       ++ +  G  N        VG+F+PI A+   + +   D HVE +   F+
Sbjct: 5   IFIASAEPYTGKSVIAFGMINMLLAKTQKVGYFKPIIAQDDPNKK---DEHVEAMLDYFS 61

Query: 123 LKGDVRAMTGVQDAEA---ARMIANGQHS-ELLDKIYSQYASYKEGQDLVLVEGPGPLMG 178
           L          +DA A     M+   + S  +++ I S+Y   ++  D  ++EG   L  
Sbjct: 62  LP------VKYEDAFAFTRQEMLHQSEDSGTIINTIISKYKKLEDNYDFTVIEGSDFLGE 115

Query: 179 GT----ELDAQIAAALNAPVLMTMTGQPNATVADYYNRAMVKRQVFLDHHVEVLGLVMNG 234
           G     E +A +A  L APVL+ ++G+ N T +  +  A+   + FL   V+VLG+V N 
Sbjct: 116 GMAFEFESNALMAKNLGAPVLIVVSGK-NKTASQLFKSAINIYRNFLLRDVQVLGVVANM 174

Query: 235 L-PRQSHAI---LSGQLRDKFAAAGLPFAGAIPTDIMLRNVRLDEVQTAMGAQRLYGDSL 290
           + P ++  I   LS QL  +   A       IPT+  L++  + E+  A+G + L+G  L
Sbjct: 175 VNPEEADRIKQALSNQLPAELLIA------VIPTETGLQSPTMKEITLALGGEVLFGSEL 228

Query: 291 LTDVEFDDVVVASQRLEELLEILAERPMGRPLVVTSADRLDIVLGLLAAQLSVSGPGVAG 350
           L D + D+ V  +  L   L  + +      L+VT  DR DI++G L A LS + P +AG
Sbjct: 229 L-DNQVDNFVTGAMMLPNFLRHIKDNL----LIVTPGDRGDIIIGALQANLSANYPKIAG 283

Query: 351 ILLTQAGSARSGRNYARDTIDRIFAGLSSSGLYKGSLLPVLVTDMPLRDAIRKLDNLDAA 410
           I+LT AGS         + I ++  GL +       ++P++       +    +  + + 
Sbjct: 284 IVLT-AGSLPD------EPIIKLIEGLQT-------IIPIIAVQKGTFETTTTIGGIHSN 329

Query: 411 ILPSSTRKISQCKRLFEQYVDANAVVARLQNMVRPNRMTPKMFMHTLKSMCNATPQHIVL 470
           I   + +KI+    LFE+YVD  A+  ++        +TP MF + L        +HIVL
Sbjct: 330 ITIENKKKIAVAIELFEKYVDIKALDDKIITFSYQG-ITPHMFQYQLVKWAKRDKKHIVL 388

Query: 471 PESEDKRVLAAAADVVQRGLAKITLLGDPTTILAEAAKLGLDL--SGCNIHNPNTSDRFD 528
           PE  D+R+L A   ++ + +  ITLLGDPT I     +LGL+L  +   IHNP  S  ++
Sbjct: 389 PEGNDERILKAVEKLITQDIVDITLLGDPTEITNTIKRLGLNLDTNTIKIHNPGQSAHYN 448

Query: 529 KYVDMLVEARKKKGMTREVAADTLHGDVNFFATMMIVAGDADGMVSGAVHTTASTVRPAL 588
            YV+ L E RK K +  E+A D +  DV++F TMM+  GDADGMVSGAVHTT  T+RPAL
Sbjct: 449 DYVNTLHELRKAKNVNLEMARDMMT-DVSYFGTMMVYKGDADGMVSGAVHTTQHTIRPAL 507

Query: 589 QVLKS-PDTPLVSSVFIMCLPDRVVVYGDCAVNVNPSAADLAQIAITSNDTAAAFGIEPR 647
           Q +K+ P   +VSS+F MCLP+RV ++GDCAVN NP+A  LA+IAI+S +++A FGIEPR
Sbjct: 508 QFVKTKPGVSVVSSIFFMCLPERVAIFGDCAVNPNPTAQQLAEIAISSAESSAKFGIEPR 567

Query: 648 VAMLSYSTLGSGSGPDVQKVSEAVAIVKQRRPDIKVEGPIQYDAAIDPKVAAVKVQGLSE 707
           +AMLSYS+  SG G DV++V EA AIVK R P++K+EGPIQYDAA+DP V   K+ G SE
Sbjct: 568 IAMLSYSSGTSGEGEDVERVREATAIVKARHPELKIEGPIQYDAAVDPLVGRQKLPG-SE 626

Query: 708 VAGKATVFIFPDLNTGNNTYKAVQQSTGAIAMGPVMQGLLRPVNDLSRGCTVPDIINTIC 767
           VAG+A+V IFPDLNTGNNTYKAVQ+ TGA+A+GP++QGL +P+NDLSRGCTV DI NT+ 
Sbjct: 627 VAGRASVLIFPDLNTGNNTYKAVQRETGALAIGPMLQGLNKPINDLSRGCTVDDIFNTVV 686

Query: 768 VTSIQ 772
           +T+IQ
Sbjct: 687 ITAIQ 691


Lambda     K      H
   0.320    0.134    0.376 

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: 1098
Number of extensions: 55
Number of successful extensions: 9
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: 792
Length of database: 695
Length adjustment: 40
Effective length of query: 752
Effective length of database: 655
Effective search space:   492560
Effective search space used:   492560
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 CA265_RS10075 CA265_RS10075 (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.10680.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   1.4e-130  421.2   0.0   2.6e-130  420.3   0.0    1.5  1  lcl|FitnessBrowser__Pedo557:CA265_RS10075  CA265_RS10075 phosphate acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS10075  CA265_RS10075 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.3   0.0  2.6e-130  2.6e-130       1     304 []     386     689 ..     386     689 .. 0.99

  Alignments for each domain:
  == domain 1  score: 420.3 bits;  conditional E-value: 2.6e-130
                                  TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyver 67 
                                                ivlPEg++er+lkA+++l++++i++ +ll++  e++++ k  ++nl+ +++++++p  s + ++yv++
  lcl|FitnessBrowser__Pedo557:CA265_RS10075 386 IVLPEGNDERILKAVEKLITQDIVDITLLGDPTEITNTiKRLGLNLDTNTIKIHNPGQSAHYNDYVNT 453
                                                8**********************************998889999************************ PP

                                  TIGR00651  68 lyekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvss 135
                                                l+e+rk+k v++++ar++++D +++++++v++g adg+vsGav+tt++t+rpalq +kt++gv++vss
  lcl|FitnessBrowser__Pedo557:CA265_RS10075 454 LHELRKAKNVNLEMARDMMTDVSYFGTMMVYKGDADGMVSGAVHTTQHTIRPALQFVKTKPGVSVVSS 521
                                                ******************************************************************** PP

                                  TIGR00651 136 vfimekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvk 203
                                                +f+m+++e+v +f+DCav+++P+a++LAeiA++sa+s  ++g +ep++a+lsys+++sg+ge+ve+v+
  lcl|FitnessBrowser__Pedo557:CA265_RS10075 522 IFFMCLPERVAIFGDCAVNPNPTAQQLAEIAISSAESSAKFG-IEPRIAMLSYSSGTSGEGEDVERVR 588
                                                ******************************************.************************* PP

                                  TIGR00651 204 eAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladae 271
                                                eA++i+k ++p+l+++G++q+DaA+ + v ++k p sevag+a v++FPdL++Gn++Yk+vqR+++a 
  lcl|FitnessBrowser__Pedo557:CA265_RS10075 589 EATAIVKARHPELKIEGPIQYDAAVDPLVGRQKLPGSEVAGRASVLIFPDLNTGNNTYKAVQRETGAL 656
                                                ******************************************************************** PP

                                  TIGR00651 272 aiGPilqGlakPvnDLsRGasvedivnvviita 304
                                                aiGP+lqGl+kP+nDLsRG++v+di+n+v+ita
  lcl|FitnessBrowser__Pedo557:CA265_RS10075 657 AIGPMLQGLNKPINDLSRGCTVDDIFNTVVITA 689
                                                *******************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (695 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 18.08
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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