Alignments for a candidate for pta in Chromobacterium vaccinii MWU205

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Chromobacterium vaccinii MWU205

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_046157845.1 VL52_RS15350 phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>NCBI__GCF_000971335.1:WP_046157845.1
          Length = 693

 Score =  830 bits (2144), Expect = 0.0
 Identities = 430/704 (61%), Positives = 545/704 (77%), Gaps = 12/704 (1%)

Query: 1   MHTFFIAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTH 60
           M TFF+APTGF  GLTS++LG +R+LE+AGL+VGF KPIAQ    D   ERS+       
Sbjct: 1   MQTFFLAPTGFNAGLTSVTLGAIRSLEQAGLRVGFVKPIAQ-DTKDGEAERSTHFAQAIC 59

Query: 61  GLDTPKPLPLAQVERMLGDGQLDELLEEIISLYQRAAADKDVVIVEGMVPTRHASYAARV 120
            L+ P+P+ + +VE +L  GQ+D+L+EE++SL+Q+A+ + DVVIVEG+VP +   ++  +
Sbjct: 60  RLNPPQPISMERVEHLLSQGQVDQLMEEVVSLFQQASQNVDVVIVEGLVPDQKQVFSTFL 119

Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRGEADAA 180
           N  +A++L A+ ILVS+ +    TE+ +++E+  Q FG      V G ILN V   AD A
Sbjct: 120 NTKIARNLQAQTILVSSVKALNATEIAEQLEMNIQAFGAQT---VSGYILNHVLPGADRA 176

Query: 181 NAEDGVADFARRLTEHSPLLRDDFRLIGCIPWQDELNAARTRDIADLLSARVINAGDYEQ 240
                  + AR + E   L +    L+G IP+Q EL A RT+D+A  L+A V++AG    
Sbjct: 177 -------ELAREVQESGNLKKAGLPLLGVIPYQQELLAPRTQDVARYLNANVVHAGQQAN 229

Query: 241 RRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAGLLLCSDFPP 300
           RRV+ +V+ AR  PN V LLKPG L++TPG+R+D+++A S+AAMNGVPLAGLLL  D  P
Sbjct: 230 RRVRNMVVAARTAPNIVNLLKPGALIITPGEREDVVMATSMAAMNGVPLAGLLLTCDSEP 289

Query: 301 DPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVTEFVAGHIDF 360
           DPRI +LC+ A  GGLPVL+ +  S +TA+ LN M+ ++P DD ER E+V E VA  +D 
Sbjct: 290 DPRIQQLCQQAFTGGLPVLATSLNSMETASALNAMSHQVPSDDLERMEKVIEHVAEFLDV 349

Query: 361 EWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAICQARGIARC 420
             LKQ  G PRE+RL PPAFR+Q++++A+KA KRIVLPEG+EPRT+QAAAICQ +GIARC
Sbjct: 350 STLKQSVGEPREIRLPPPAFRFQLMEKARKANKRIVLPEGNEPRTIQAAAICQEKGIARC 409

Query: 421 VLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNAPMAEQQLED 480
           VLL    E+  VA+ QG+ LPE +EI+DP+ +R +YV PMVELRKGKGLN PMA  QLED
Sbjct: 410 VLLGNRAEILQVAETQGVTLPESVEILDPNEIRGQYVGPMVELRKGKGLNEPMALAQLED 469

Query: 481 SVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFMLLPDQVLVY 540
           +VVL TMMLA++EVDGLVSGA+HTTA+TIRPALQLIKTAPG ++VSSVFFML+P+QV VY
Sbjct: 470 TVVLGTMMLAMNEVDGLVSGAVHTTANTIRPALQLIKTAPGSSIVSSVFFMLMPEQVYVY 529

Query: 541 GDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVDKVREATRLA 600
           GDCAVNPDP+A  LA+IA+QSA SA AFGI  RVAMISYSTG SGSG DV+KVREATR+A
Sbjct: 530 GDCAVNPDPTAEQLADIAIQSADSAVAFGITPRVAMISYSTGSSGSGSDVEKVREATRIA 589

Query: 601 REQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTTYKAVQRSAD 660
           +E+RPDLLIDGP+QYDAA++ SVGRQKAP+S VAG+ATVF+FPDLNTGNTTYKAVQRSA+
Sbjct: 590 QEKRPDLLIDGPMQYDAASVESVGRQKAPDSQVAGRATVFVFPDLNTGNTTYKAVQRSAN 649

Query: 661 CVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQADAQAPA 704
            VSVGPMLQGLRKPVNDLSRGALV+DIVYTIALTA+QA+ Q PA
Sbjct: 650 VVSVGPMLQGLRKPVNDLSRGALVDDIVYTIALTALQAE-QTPA 692


Lambda     K      H
   0.319    0.136    0.388 

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: 1205
Number of extensions: 40
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: 704
Length of database: 693
Length adjustment: 39
Effective length of query: 665
Effective length of database: 654
Effective search space:   434910
Effective search space used:   434910
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_046157845.1 VL52_RS15350 (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.3592415.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-133  429.6   0.5   5.9e-133  429.0   0.1    1.5  2  NCBI__GCF_000971335.1:WP_046157845.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000971335.1:WP_046157845.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0      0.26      0.26     130     191 ..     264     327 ..     232     344 .. 0.56
   2 !  429.0   0.1  5.9e-133  5.9e-133       1     304 []     384     684 ..     384     684 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.26
                             TIGR00651 130 vklvssvfimekeeevlvfaDCavavdPnaeeLAeiAlqsa..ksakslgeeepkvallsystk 191
                                           v ++ s+  m+      +   C   +dP  ++L + A +      a sl+  e   al + s +
  NCBI__GCF_000971335.1:WP_046157845.1 264 VVMATSMAAMNGVPLAGLLLTCDSEPDPRIQQLCQQAFTGGlpVLATSLNSMETASALNAMSHQ 327
                                           4444455555544444444457777888888887777665311345555555555565555554 PP

  == domain 2  score: 429.0 bits;  conditional E-value: 5.9e-133
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           ivlPEg+e+r+++Aaa+++ek+ia++vll+n +e+ ++ ++++v l   +v++ dp+    + +yv  ++e+r
  NCBI__GCF_000971335.1:WP_046157845.1 384 IVLPEGNEPRTIQAAAICQEKGIARCVLLGNRAEILQVaETQGVTLPE-SVEILDPNEI--RGQYVGPMVELR 453
                                           8************************************96677777665.5667777766..69********** PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           k kG++e +a  ql+D+v+l++++++++e+dglvsGav+tta+t+rpalq+ikt++g+++vssvf+m  +e+v
  NCBI__GCF_000971335.1:WP_046157845.1 454 KGKGLNEPMALAQLEDTVVLGTMMLAMNEVDGLVSGAVHTTANTIRPALQLIKTAPGSSIVSSVFFMLMPEQV 526
                                           ************************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                           +v++DCav++dP+ae+LA+iA+qsa+sa ++g + p+va++syst++sg+g++vekv+eA++i++ek+pdll+
  NCBI__GCF_000971335.1:WP_046157845.1 527 YVYGDCAVNPDPTAEQLADIAIQSADSAVAFG-ITPRVAMISYSTGSSGSGSDVEKVREATRIAQEKRPDLLI 598
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           dG++q+DaA ve+v ++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+a++ ++GP+lqGl+kPvnDLsRGa
  NCBI__GCF_000971335.1:WP_046157845.1 599 DGPMQYDAASVESVGRQKAPDSQVAGRATVFVFPDLNTGNTTYKAVQRSANVVSVGPMLQGLRKPVNDLSRGA 671
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v+div+++++ta
  NCBI__GCF_000971335.1:WP_046157845.1 672 LVDDIVYTIALTA 684
                                           ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (693 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: 28.19
//
[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