Alignments for a candidate for pta in Paludibacter propionicigenes WB4

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Paludibacter propionicigenes WB4

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_013445572.1 PALPR_RS10355 phosphate acetyltransferase

Query= metacyc::PTACLOS-MONOMER
         (333 letters)



>NCBI__GCF_000183135.1:WP_013445572.1
          Length = 333

 Score =  373 bits (957), Expect = e-108
 Identities = 190/332 (57%), Positives = 247/332 (74%), Gaps = 1/332 (0%)

Query: 1   MDLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELN 60
           MDL+E+I   AK + +RI+L EG E R L AAD I+KE  A+L+L+G+EN+IK+ A+E N
Sbjct: 1   MDLLENIMARAKANLQRIVLPEGTEIRTLKAADIILKEKAAKLILIGNENEIKKLAAENN 60

Query: 61  LD-ISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVD 119
           L  I++A I+DPET +K   Y+   +ELRK KGMTIE++ K+ ++PLY   + +K+G  D
Sbjct: 61  LTHIAEATIVDPETDVKMGDYSNLLFELRKSKGMTIEEATKLAKNPLYLGCLMIKNGDAD 120

Query: 120 GMVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNP 179
           G ++GA +TTG++LRP  QI+KT PG+ +VSG  +M  P   YGE GLL+FADCAVNPNP
Sbjct: 121 GELAGAQNTTGNVLRPAFQIVKTLPGINVVSGALLMFTPTPQYGENGLLVFADCAVNPNP 180

Query: 180 TSDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLA 239
           T+ ELA IA+ TAETAR +C  EP+VAMLSFS+ GSAK E+VDKV  A  + K+  P+L 
Sbjct: 181 TAPELAQIAVCTAETARVICGYEPRVAMLSFSSKGSAKHELVDKVVEATRLAKEMAPELM 240

Query: 240 IDGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPIC 299
           IDGELQ DAA+   V   KAP S +AG+ANVLVFPDLQ GNI YKLV+RF+ A+A+GPI 
Sbjct: 241 IDGELQADAALVPSVGQSKAPGSQIAGHANVLVFPDLQAGNIAYKLVERFSGAQAVGPIL 300

Query: 300 QGFAKPINDLSRGCSSEDIVNVVAITVVQAQR 331
           QG A PINDLSRGCS +DIV ++ IT  QA +
Sbjct: 301 QGMAAPINDLSRGCSVDDIVRMITITANQAMK 332


Lambda     K      H
   0.316    0.134    0.374 

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: 336
Number of extensions: 8
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: 333
Length of database: 333
Length adjustment: 28
Effective length of query: 305
Effective length of database: 305
Effective search space:    93025
Effective search space used:    93025
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 (21.6 bits)
S2: 49 (23.5 bits)

Align candidate WP_013445572.1 PALPR_RS10355 (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.1209914.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.1e-118  379.1   0.2     1e-117  378.9   0.2    1.0  1  NCBI__GCF_000183135.1:WP_013445572.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000183135.1:WP_013445572.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.9   0.2    1e-117    1e-117       1     304 []      18     327 ..      18     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 378.9 bits;  conditional E-value: 1e-117
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           ivlPEg+e r+lkAa +++++k a+ +l++n++e++k +a++  +++++ +++dp++  ++ +y + l+e+rk
  NCBI__GCF_000183135.1:WP_013445572.1  18 IVLPEGTEIRTLKAADIILKEKAAKLILIGNENEIKKLAAENNLTHIAEATIVDPETDVKMGDYSNLLFELRK 90 
                                           8**********************************9988888889999************************* PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee... 143
                                            kG+t +ea +  +++++l+ l+++ g adg+ +Ga++tt ++lrpa+qi+ktl+g+++vs+ ++m ++    
  NCBI__GCF_000183135.1:WP_013445572.1  91 SKGMTIEEATKLAKNPLYLGCLMIKNGDADGELAGAQNTTGNVLRPAFQIVKTLPGINVVSGALLMFTPTpqy 163
                                           *******************************************************************999899 PP

                             TIGR00651 144 ...evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkeke 213
                                              ++lvfaDCav+++P+a eLA+iA+ +a++a+ + + ep+va+ls+s+kgs+k e v+kv+eA++++ke +
  NCBI__GCF_000183135.1:WP_013445572.1 164 genGLLVFADCAVNPNPTAPELAQIAVCTAETARVICGYEPRVAMLSFSSKGSAKHELVDKVVEATRLAKEMA 236
                                           9999********************************************************************* PP

                             TIGR00651 214 pdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnD 286
                                           p+l++dGelq DaAlv++v ++kap s++ag+anv+vFPdL+aGni+Yk+v+R+++a+a+GPilqG+a P+nD
  NCBI__GCF_000183135.1:WP_013445572.1 237 PELMIDGELQADAALVPSVGQSKAPGSQIAGHANVLVFPDLQAGNIAYKLVERFSGAQAVGPILQGMAAPIND 309
                                           ************************************************************************* PP

                             TIGR00651 287 LsRGasvedivnvviita 304
                                           LsRG+sv+div ++ ita
  NCBI__GCF_000183135.1:WP_013445572.1 310 LSRGCSVDDIVRMITITA 327
                                           **************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (333 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: 11.58
//
[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