Alignments for a candidate for pta in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Moritella dasanensis ArB 0140

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate WP_017220614.1 A923_RS0105275 phosphate acetyltransferase

Query= BRENDA::Q8ZND6
         (714 letters)



>NCBI__GCF_000276805.1:WP_017220614.1
          Length = 709

 Score =  972 bits (2512), Expect = 0.0
 Identities = 482/706 (68%), Positives = 589/706 (83%)

Query: 6   MLIPTGTSVGLTSVSLGVIRAMERKGVRLSVFKPIAQPRAGGDAPDQTTTIVRANSTLPA 65
           MLIP G  VG+TSVSLG++RA ER G+ ++ FKP+AQPR G   P+ +T I+R  +    
Sbjct: 1   MLIPVGVGVGVTSVSLGMVRAFERNGLNVNFFKPVAQPRQGEKGPELSTEIIRQGTNASP 60

Query: 66  AEPLKMSHVESLLSSNQKDVLMEEIIANYHANTKDAEVVLVEGLVPTRKHQFAQSLNYEI 125
           A P  +SH E L+ + + DVL+E+I+  + ++  DAE+V+VEGLVPT K  FA  +NY I
Sbjct: 61  ATPFTLSHAEKLIGAGKTDVLLEDIVERFESHMVDAEIVVVEGLVPTSKQPFANDVNYNI 120

Query: 126 AKTLNAEIVFVMSQGTDTPEQLNERIELTRSSFGGAKNTNITGVIINKLNAPVDEQGRTR 185
           AK L+AE+VFV + GTD+ EQL +R+E+  S+FGG+KN NI G +INK+ AP+DE GR+R
Sbjct: 121 AKALDAEMVFVTNPGTDSSEQLKDRLEIACSNFGGSKNKNIIGCVINKVGAPLDEAGRSR 180

Query: 186 PDLSEIFDDSSKAQVIKIDPAKLQESSPLPVLGAVPWSFDLIATRAIDMARHLNATIINE 245
           PDL+E+F+ ++      ++  ++   SP+P+LG +PWS +LIA RA D+A+HL A I+NE
Sbjct: 181 PDLAEMFEANAGNASHNLEVLQVFGKSPMPILGCIPWSAELIAPRAKDLAKHLGAEILNE 240

Query: 246 GDIKTRRVKSVTFCARSIPHMLEHFRAGSLLVTSADRPDVLVAACLAAMNGVEIGALLLT 305
           GDI+ RR+  +TFCARSIP+MLEHFR G LLVTS DR DV+VAACLAAMNGV+IGALLLT
Sbjct: 241 GDIEERRLVGITFCARSIPNMLEHFRPGGLLVTSGDRADVIVAACLAAMNGVKIGALLLT 300

Query: 306 GGYEMDARISKLCERAFATGLPVFMVNTNTWQTSLSLQSFNLEVPVDDHERIEKVQEYVA 365
           G    DA + KLC++A ATGLP+ +  TNTWQT+L+LQ+FNL++P DD +RIE VQEY+A
Sbjct: 301 GDVRPDASVLKLCQQAMATGLPIMLTPTNTWQTALTLQNFNLDIPADDKQRIEAVQEYIA 360

Query: 366 NYVNAEWIESLTATSERSRRLSPPAFRYQLTELARKAGKRVVLPEGDEPRTVKAAAICAE 425
           ++++ +WIESLT  ++R+RRLSPPAFRYQLTELAR+A KRVVLPEG+EPRT++AA ICAE
Sbjct: 361 SHIDKQWIESLTVGTQRTRRLSPPAFRYQLTELARQAKKRVVLPEGEEPRTIEAANICAE 420

Query: 426 RGIATCVLLGNPDEINRVAASQGVELGAGIEIVDPEVVRESYVARLVELRKSKGMTEPVA 485
           RGIAT VLLGNP EI RVA SQG+ L  G+EI+DP    E YVA +VELRK+KG+TE VA
Sbjct: 421 RGIATPVLLGNPAEIKRVAESQGIILSDGVEIIDPVTCLEKYVAPMVELRKAKGLTEVVA 480

Query: 486 REQLEDNVVLGTLMLEQDEVDGLVSGAVHTTANTIRPPLQLIKTAPGSSLVSSVFFMLLP 545
           REQL+D+VVL T+MLEQ EVDGLVSGAVHTTANTIRP LQLIKTAPGS+LVSS+FFMLLP
Sbjct: 481 REQLQDSVVLATMMLEQAEVDGLVSGAVHTTANTIRPALQLIKTAPGSNLVSSIFFMLLP 540

Query: 546 EQVYVYGDCAINPDPTAEQLAEIAIQSADSAIAFGIEPRVAMLSYSTGTSGAGSDVEKVR 605
           +QV VYGDCAINPDP A QLA+IAIQSADSA AFGI+PRVAM+SYSTG+SG GSDVEKVR
Sbjct: 541 DQVLVYGDCAINPDPDASQLADIAIQSADSAKAFGIDPRVAMISYSTGSSGQGSDVEKVR 600

Query: 606 EATRLAQEKRPDLMIDGPLQYDAAVMADVAKSKAPNSPVAGRATVFIFPDLNTGNTTYKA 665
           EAT+LAQE+RPDL+IDGPLQYDAA+M +VAKSKAPNSPVAG+ATVF+FPDLNTGNTTYKA
Sbjct: 601 EATKLAQERRPDLIIDGPLQYDAAIMENVAKSKAPNSPVAGKATVFVFPDLNTGNTTYKA 660

Query: 666 VQRSADLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQASQ 711
           VQRSA+LISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQA Q
Sbjct: 661 VQRSANLISIGPMLQGMRKPVNDLSRGALVDDIVYTIALTAIQAKQ 706


Lambda     K      H
   0.316    0.131    0.364 

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: 1300
Number of extensions: 44
Number of successful extensions: 1
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: 709
Length adjustment: 39
Effective length of query: 675
Effective length of database: 670
Effective search space:   452250
Effective search space used:   452250
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_017220614.1 A923_RS0105275 (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.3680294.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-137  443.4   0.3   3.4e-137  442.9   0.3    1.2  1  NCBI__GCF_000276805.1:WP_017220614.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000276805.1:WP_017220614.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.9   0.3  3.4e-137  3.4e-137       1     304 []     401     701 ..     401     701 .. 0.97

  Alignments for each domain:
  == domain 1  score: 442.9 bits;  conditional E-value: 3.4e-137
                             TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverlyekr 72 
                                           +vlPEg+e+r+++Aa+++ae++ia++vll+n +e++++ +++++ l    v+++dp +   +ekyv  ++e+r
  NCBI__GCF_000276805.1:WP_017220614.1 401 VVLPEGEEPRTIEAANICAERGIATPVLLGNPAEIKRVaESQGIIL-SDGVEIIDPVTC--LEKYVAPMVELR 470
                                           69***********************************845555544.456788888888..8*********** PP

                             TIGR00651  73 khkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfimekeeev 145
                                           k+kG+te  areql+D+v+la++++e+ e+dglvsGav+tta+t+rpalq+ikt++g++lvss+f+m ++++v
  NCBI__GCF_000276805.1:WP_017220614.1 471 KAKGLTEVVAREQLQDSVVLATMMLEQAEVDGLVSGAVHTTANTIRPALQLIKTAPGSNLVSSIFFMLLPDQV 543
                                           ************************************************************************* PP

                             TIGR00651 146 lvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAvkilkekepdlll 218
                                           lv++DCa+++dP+a +LA+iA+qsa+sak++g ++p+va++syst++sg+g++vekv+eA+k+++e++pdl +
  NCBI__GCF_000276805.1:WP_017220614.1 544 LVYGDCAINPDPDASQLADIAIQSADSAKAFG-IDPRVAMISYSTGSSGQGSDVEKVREATKLAQERRPDLII 615
                                           ********************************.**************************************** PP

                             TIGR00651 219 dGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGPilqGlakPvnDLsRGa 291
                                           dG+lq+DaA++e+va++kap+s+vagka+vfvFPdL++Gn++Yk+vqR+a++ +iGP+lqG++kPvnDLsRGa
  NCBI__GCF_000276805.1:WP_017220614.1 616 DGPLQYDAAIMENVAKSKAPNSPVAGKATVFVFPDLNTGNTTYKAVQRSANLISIGPMLQGMRKPVNDLSRGA 688
                                           ************************************************************************* PP

                             TIGR00651 292 svedivnvviita 304
                                           +v+div+++++ta
  NCBI__GCF_000276805.1:WP_017220614.1 689 LVDDIVYTIALTA 701
                                           ***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (709 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: 56.22
//
[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)
Organisms (tab-delimited)
SQLite3 databases

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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