Alignments for a candidate for pta in Psychromonas ingrahamii 37

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Psychromonas ingrahamii 37

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_011771551.1 PING_RS17090 phosphate acetyltransferase

Query= BRENDA::P0A9M8
         (714 letters)



>NCBI__GCF_000015285.1:WP_011771551.1
          Length = 720

 Score =  951 bits (2459), Expect = 0.0
 Identities = 470/712 (66%), Positives = 586/712 (82%), Gaps = 1/712 (0%)

Query: 1   MSRIIMLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRTGGDAPDQTTTIVRAN 60
           M R IMLIP G+ VG+TSVSLG++RA+ER+GV ++ FKPIAQPR+G   P+++T  +R N
Sbjct: 1   MPRTIMLIPIGSGVGVTSVSLGMVRALERQGVAVNFFKPIAQPRSGDVGPERSTATLR-N 59

Query: 61  SSTTTAAEPLKMSYVEGLLSSNQKDVLMEEIVANYHANTKDAEVVLVEGLVPTRKHQFAQ 120
           +S     EP  M Y E L+SS++   L+E IV  +   TK+++V++VEGLVPT KHQFA 
Sbjct: 60  ASALNPPEPFAMKYAENLISSSRTSELLENIVERFRQGTKESDVIIVEGLVPTDKHQFAN 119

Query: 121 SLNYEIAKTLNAEIVFVMSQGTDTPEQLKERIELTRNSFGGAKNTNITGVIVNKLNAPVD 180
            +NY IAK L AE+VFV     DT +QLKERIE+  +SFGG  N  I G I+NK+ AP D
Sbjct: 120 EINYSIAKALGAEMVFVTHPNNDTSQQLKERIEIAVSSFGGKNNQRIAGCIINKVGAPSD 179

Query: 181 EQGRTRPDLSEIFDDSSKAKVNNVDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLN 240
           E  + RPDL+E+F+ +  +  +N++  ++   SPLP+LG +PWS +LIA R +D+A HL+
Sbjct: 180 ESEQYRPDLTEMFEGAHDSLNSNLEVLQMFSKSPLPILGCIPWSSELIAPRVVDLATHLH 239

Query: 241 ATIINEGDINTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEI 300
           A I+N+GD+NTRR++ VTFCARSIP+MLEHF+AGS+LVTS DR DV++AACLA MNG++I
Sbjct: 240 AKILNKGDLNTRRLQRVTFCARSIPNMLEHFKAGSMLVTSGDRSDVIIAACLAVMNGMKI 299

Query: 301 GALLLTGGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEK 360
           G LLLTG Y  +A + KLC RA  +GLP+ ++N+NTWQT+  LQ+FN+E+PVDD ERIEK
Sbjct: 300 GCLLLTGDYTPEAEVMKLCARAMESGLPILLINSNTWQTAQRLQNFNMEIPVDDIERIEK 359

Query: 361 VQEYVANYINADWIESLTATSERSRRLSPPAFRYQLTELARKAGKRIVLPEGDEPRTVKA 420
           VQEY+A +++  W+++LT  S  SRRLSPPAFRY LTELARK  +RIVLPEG+EPRT++A
Sbjct: 360 VQEYIAGHVDKHWLKTLTGDSSLSRRLSPPAFRYHLTELARKNSQRIVLPEGEEPRTIQA 419

Query: 421 AAICAERGIATCVLLGNPAEINRVAASQGVELGAGIEIVDPEVVRESYVGRLVELRKNKG 480
           A ICA+RGIA  VLLGNP EI+RVA  QG+ L   +EI++P+ V E YV  +VELRK+KG
Sbjct: 420 ALICAQRGIAKPVLLGNPEEIHRVATQQGIVLTDDVEIINPDDVIEDYVAPMVELRKSKG 479

Query: 481 MTETVAREQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSV 540
           +TE VAREQL D VVLGT+ML + EV GLVSGA++TTANTIRP LQLIKTAPG++LVSS+
Sbjct: 480 LTEVVAREQLRDTVVLGTMMLAEGEVSGLVSGALNTTANTIRPALQLIKTAPGANLVSSI 539

Query: 541 FFMLLPEQVYVYGDCAINPDPTAEQLAEIAIQSADSAAAFGIEPRVAMLSYSTGTSGAGS 600
           FFMLLP+QV VYGDCAINPDP+AEQLA+IAIQSADSA AFGI+P+VAM+SYSTGTSG GS
Sbjct: 540 FFMLLPDQVLVYGDCAINPDPSAEQLADIAIQSADSAIAFGIDPKVAMISYSTGTSGVGS 599

Query: 601 DVEKVREATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTG 660
           DV+KVREAT++AQ++RPDL+IDGPLQYDAAVM +VAKSKAP+SPVAG+ATVFIFPDLNTG
Sbjct: 600 DVDKVREATKIAQQRRPDLLIDGPLQYDAAVMENVAKSKAPDSPVAGKATVFIFPDLNTG 659

Query: 661 NTTYKAVQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQSAQ 712
           NTTYKAVQRSA+LISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQ+ Q
Sbjct: 660 NTTYKAVQRSANLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQATQ 711


Lambda     K      H
   0.316    0.131    0.363 

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: 1309
Number of extensions: 43
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: 714
Length of database: 720
Length adjustment: 40
Effective length of query: 674
Effective length of database: 680
Effective search space:   458320
Effective search space used:   458320
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: 55 (25.8 bits)

Align candidate WP_011771551.1 PING_RS17090 (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.3683400.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-134  434.6   0.2   5.3e-134  432.4   0.2    1.9  2  NCBI__GCF_000015285.1:WP_011771551.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015285.1:WP_011771551.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.034     0.034      19      78 ..     322     377 ..     309     385 .. 0.71
   2 !  432.4   0.2  5.3e-134  5.3e-134       1     304 []     406     706 ..     406     706 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.034
                             TIGR00651  19 aekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrkhkGvt 78 
                                           +e+++  ++ll+n+++ ++  a+++++   ++ v+d +  +++++y+   ++k+  k +t
  NCBI__GCF_000015285.1:WP_011771551.1 322 MESGL--PILLINSNTWQT--AQRLQNFNMEIPVDDIERIEKVQEYIAGHVDKHWLKTLT 377
                                           44444..678888877776..666666666778888888889999999999998888665 PP

  == domain 2  score: 432.4 bits;  conditional E-value: 5.3e-134
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlyekrk 73 
                                           ivlPEg+e+r+++Aa ++a+++ia++vll+n ee++++++++      +v++++pd    ie+yv  ++e+rk
  NCBI__GCF_000015285.1:WP_011771551.1 406 IVLPEGEEPRTIQAALICAQRGIAKPVLLGNPEEIHRVATQQGIVLTDDVEIINPDDV--IEDYVAPMVELRK 476
                                           8************************************965555555667777777777..7************ PP

                             TIGR00651  74 hkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeevl 146
                                            kG+te  areqlrD+v+l++++++ ge+ glvsGa +tta+t+rpalq+ikt++g +lvss+f+m ++++vl
  NCBI__GCF_000015285.1:WP_011771551.1 477 SKGLTEVVAREQLRDTVVLGTMMLAEGEVSGLVSGALNTTANTIRPALQLIKTAPGANLVSSIFFMLLPDQVL 549
                                           ************************************************************************* PP

                             TIGR00651 147 vfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdllld 219
                                           v++DCa+++dP+ae+LA+iA+qsa+sa ++g ++pkva++syst++sg g++v+kv+eA+ki+++++pdll+d
  NCBI__GCF_000015285.1:WP_011771551.1 550 VYGDCAINPDPSAEQLADIAIQSADSAIAFG-IDPKVAMISYSTGTSGVGSDVDKVREATKIAQQRRPDLLID 621
                                           *******************************.***************************************** PP

                             TIGR00651 220 GelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGas 292
                                           G+lq+DaA++e+va++kap+s+vagka+vf+FPdL++Gn++Yk+vqR+a++ +iGP+lqG++kPvnDLsRGa+
  NCBI__GCF_000015285.1:WP_011771551.1 622 GPLQYDAAVMENVAKSKAPDSPVAGKATVFIFPDLNTGNTTYKAVQRSANLISIGPMLQGMRKPVNDLSRGAL 694
                                           ************************************************************************* PP

                             TIGR00651 293 vedivnvviita 304
                                           v+div+++++ta
  NCBI__GCF_000015285.1:WP_011771551.1 695 VDDIVYTIALTA 706
                                           **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (720 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 28.02
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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