Alignments for a candidate for pta in Rubrivirga marina SAORIC-28

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Rubrivirga marina SAORIC-28

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_095510994.1 BSZ37_RS13165 phosphate acetyltransferase

Query= BRENDA::O52593
         (332 letters)



>NCBI__GCF_002283365.1:WP_095510994.1
          Length = 331

 Score =  273 bits (697), Expect = 6e-78
 Identities = 149/322 (46%), Positives = 206/322 (63%), Gaps = 8/322 (2%)

Query: 9   ERAKSDVKTIVLPESTDLRVIKAASMIMKKGIAKVVLIGNEKEIKSLAGDIDLE---GVM 65
           +RA++  K I LPE  D R I+AA+ + +  + + +LIG E +I++ A  + +     V 
Sbjct: 12  DRARALKKRIALPEGEDPRTIRAAAWLAEHEVVRPLLIGREAQIRAEADRLGVSLPHSVP 71

Query: 66  IEDSLNSEKLEDYANTLYELRKSKGMTIEAARETIKDPLYYGVMMVKKGEADGMVAGAVN 125
           I D   SE+ + YA  L++ RK KG+T E A E  +D LY+G +MV  G+ADG VAGA +
Sbjct: 72  IVDPAQSERSQTYAQALFQKRKHKGLTYEQAGEWTQDVLYFGDLMVDAGDADGCVAGAAH 131

Query: 126 STANTLRPALQILKTAPGTKLVSSFFVMVVPNCEYGHNGTFVYADCGLVENPDADQLSEI 185
            + + +R A+ +L  A G+ LVSSFF+MV+P+          YADCG+  +P A+QL+ I
Sbjct: 132 PSPDVIRAAIHVLGVAEGSALVSSFFLMVLPD-----GRPLTYADCGVNADPSAEQLASI 186

Query: 186 AISASKSFEMLVGAKPQVAMLSYSSYGSAKSELTEKVIKATQLAKEKAPHLAIDGELQVD 245
            + A+ +   L G +P VA LS+S+ GSA     +KV +A ++A+ K P LA+DGE Q D
Sbjct: 187 GLDAAANHRFLTGQEPVVAFLSFSTKGSADHPDVDKVREAVEIARRKKPDLALDGEFQFD 246

Query: 246 AAIVPEVAKSKAKGSSVAGKANVLIFPDLDAGNIAYKLTQRLAKAEAYGPITQGLARPVN 305
           AA    V + KA GS VAGKANV +FPDL AGNI YK+TQR+  AEA+GP+ QGL  P N
Sbjct: 247 AAFDAGVGERKAPGSPVAGKANVYVFPDLGAGNIGYKITQRVGGAEAFGPVLQGLRLPAN 306

Query: 306 DLSRGCSAEDIVGVAAITAVQA 327
           DLSRG   EDI  VA ITA+QA
Sbjct: 307 DLSRGADWEDIANVATITAIQA 328


Lambda     K      H
   0.313    0.129    0.346 

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: 250
Number of extensions: 11
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: 332
Length of database: 331
Length adjustment: 28
Effective length of query: 304
Effective length of database: 303
Effective search space:    92112
Effective search space used:    92112
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate WP_095510994.1 BSZ37_RS13165 (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.3484622.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-109  351.7   0.0   2.3e-109  351.5   0.0    1.0  1  NCBI__GCF_002283365.1:WP_095510994.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002283365.1:WP_095510994.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.5   0.0  2.3e-109  2.3e-109       1     304 []      21     325 ..      21     325 .. 0.97

  Alignments for each domain:
  == domain 1  score: 351.5 bits;  conditional E-value: 2.3e-109
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgk.vvvedpdvskdiekyverlyekr 72 
                                           i lPEg+++r+++Aaa lae++++++ l+++++++ + +a+++  +l + v ++dp  s+  ++y+++l++kr
  NCBI__GCF_002283365.1:WP_095510994.1  21 IALPEGEDPRTIRAAAWLAEHEVVRPLLIGREAQIRA-EADRLGVSLPHsVPIVDPAQSERSQTYAQALFQKR 92 
                                           679***********************99999988887.9*****999772569******************** PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekee.e 144
                                           khkG+t ++a e  +D ++++ l+v++g adg+v+Ga++ + +++r+a+++++ +eg+ lvss+f+m +++ +
  NCBI__GCF_002283365.1:WP_095510994.1  93 KHKGLTYEQAGEWTQDVLYFGDLMVDAGDADGCVAGAAHPSPDVIRAAIHVLGVAEGSALVSSFFLMVLPDgR 165
                                           *********************************************************************9945 PP

                             TIGR00651 145 vlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdll 217
                                            l +aDC v+ dP+ae+LA i l++a+  + l+++ep va+ls+stkgs+   +v+kv+eAv+i++ k+pdl+
  NCBI__GCF_002283365.1:WP_095510994.1 166 PLTYADCGVNADPSAEQLASIGLDAAANHRFLTGQEPVVAFLSFSTKGSADHPDVDKVREAVEIARRKKPDLA 238
                                           69*********************************************************************** PP

                             TIGR00651 218 ldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRG 290
                                           ldGe+qfDaA+ + v e+kap s+vagkanv+vFPdL aGnigYki qR+++aea+GP+lqGl+ P nDLsRG
  NCBI__GCF_002283365.1:WP_095510994.1 239 LDGEFQFDAAFDAGVGERKAPGSPVAGKANVYVFPDLGAGNIGYKITQRVGGAEAFGPVLQGLRLPANDLSRG 311
                                           ************************************************************************* PP

                             TIGR00651 291 asvedivnvviita 304
                                           a  edi nv+ ita
  NCBI__GCF_002283365.1:WP_095510994.1 312 ADWEDIANVATITA 325
                                           ***********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (331 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: 21.43
//
[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