Alignments for a candidate for pta in Carboxydothermus pertinax Ug1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Carboxydothermus pertinax Ug1

Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate WP_075860088.1 cpu_RS11365 phosphate acetyltransferase

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



>NCBI__GCF_001950255.1:WP_075860088.1
          Length = 334

 Score =  350 bits (899), Expect = e-101
 Identities = 174/333 (52%), Positives = 245/333 (73%)

Query: 1   MDLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELN 60
           ++ IE +   A++ ++ IIL E ++ R + AA +IIK+ LA+++L+G+E +I E+A  LN
Sbjct: 2   LNFIEKVKSTAREFQRTIILPESKDDRVIKAAGEIIKQQLAKIILLGNEKEIAERAKNLN 61

Query: 61  LDISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVDG 120
           +++    +++P T  + + YA   YE+RK KGMT++K+ +++ +PLYFAT+ +K    DG
Sbjct: 62  VNLDGVVVVNPLTDSRRDRYANLLYEVRKSKGMTLDKAYELLNNPLYFATLMVKAEDADG 121

Query: 121 MVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNPT 180
           +V+G++  T D+LRP LQIIKT P   +VSG F+M+IP+  +GE G++LFADCAVNP+P 
Sbjct: 122 LVAGSLSPTPDVLRPALQIIKTKPEFSVVSGAFIMVIPNPQFGEHGIMLFADCAVNPDPN 181

Query: 181 SDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLAI 240
             +LA+IAI +A TA+KL  + P V +LSFST GSA+ E+V+KV+ AV I    RPDL I
Sbjct: 182 PQQLAEIAIASAMTAQKLLGITPYVGLLSFSTKGSAEHELVEKVREAVRIANALRPDLKI 241

Query: 241 DGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPICQ 300
           +GELQ+DAAI   V A KAP S VAG ANVL+FPDLQ+GNIGYKL QR +  +AIGPI Q
Sbjct: 242 EGELQVDAAIVPAVGAQKAPGSEVAGRANVLIFPDLQSGNIGYKLAQRMSGGEAIGPILQ 301

Query: 301 GFAKPINDLSRGCSSEDIVNVVAITVVQAQRGI 333
           G AKP+NDLSRGCS ++IVN+ AIT VQ+  GI
Sbjct: 302 GMAKPVNDLSRGCSVDEIVNLTAITAVQSYYGI 334


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: 15
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: 334
Length adjustment: 28
Effective length of query: 305
Effective length of database: 306
Effective search space:    93330
Effective search space used:    93330
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_075860088.1 cpu_RS11365 (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.556440.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.1e-121  390.5   0.1   3.5e-121  390.3   0.1    1.0  1  NCBI__GCF_001950255.1:WP_075860088.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001950255.1:WP_075860088.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.3   0.1  3.5e-121  3.5e-121       1     304 []      19     327 ..      19     327 .. 0.99

  Alignments for each domain:
  == domain 1  score: 390.3 bits;  conditional E-value: 3.5e-121
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           i+lPE+++ rv+kAa  ++++++a+ +ll+n++e+ + +ak++n +l  vvv++p +   +++y++ lye rk
  NCBI__GCF_001950255.1:WP_075860088.1  19 IILPESKDDRVIKAAGEIIKQQLAKIILLGNEKEIAE-RAKNLNVNLDGVVVVNPLTDSRRDRYANLLYEVRK 90 
                                           8***************************999999988.9********************************** PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee... 143
                                            kG+t+ +a e l++++++a+l+v+++ adglv+G+ s t ++lrpalqiikt++ +++vs+ fim  ++   
  NCBI__GCF_001950255.1:WP_075860088.1  91 SKGMTLDKAYELLNNPLYFATLMVKAEDADGLVAGSLSPTPDVLRPALQIIKTKPEFSVVSGAFIMVIPNpqf 163
                                           ********************************************************************99999 PP

                             TIGR00651 144 ...evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkeke 213
                                              ++++faDCav++dPn+++LAeiA+ sa +a++l ++ p v lls+stkgs++ e vekv+eAv+i++  +
  NCBI__GCF_001950255.1:WP_075860088.1 164 gehGIMLFADCAVNPDPNPQQLAEIAIASAMTAQKLLGITPYVGLLSFSTKGSAEHELVEKVREAVRIANALR 236
                                           9999********************************************************************* PP

                             TIGR00651 214 pdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnD 286
                                           pdl+++Gelq DaA+v+ v ++kap sevag+anv++FPdL++GnigYk++qR+++ eaiGPilqG+akPvnD
  NCBI__GCF_001950255.1:WP_075860088.1 237 PDLKIEGELQVDAAIVPAVGAQKAPGSEVAGRANVLIFPDLQSGNIGYKLAQRMSGGEAIGPILQGMAKPVND 309
                                           ************************************************************************* PP

                             TIGR00651 287 LsRGasvedivnvviita 304
                                           LsRG+sv++ivn+++ita
  NCBI__GCF_001950255.1:WP_075860088.1 310 LSRGCSVDEIVNLTAITA 327
                                           ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (334 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: 22.82
//
[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