Alignments for a candidate for pta in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for pta in Halomonas desiderata SP1

Align Phosphate acetyltransferase; Phosphotransacetylase; EC 2.3.1.8 (characterized)
to candidate WP_086512002.1 BZY95_RS21875 phosphate acetyltransferase

Query= SwissProt::Q9I5A5
         (704 letters)



>NCBI__GCF_002151265.1:WP_086512002.1
          Length = 724

 Score =  806 bits (2082), Expect = 0.0
 Identities = 428/707 (60%), Positives = 523/707 (73%), Gaps = 15/707 (2%)

Query: 6   IAPTGFGVGLTSISLGLLRALERAGLKVGFFKPIAQLHPGDLGPERSSELVARTHGLDTP 65
           + PTG GVGLTS  LGL++AL+  GLK GF KP  Q      GP+RS+ LV  T G+  P
Sbjct: 15  MVPTGVGVGLTSACLGLMQALDTIGLKAGFLKPFRQDELNGPGPDRSTALVGSTLGMRPP 74

Query: 66  KPLPLAQVERMLGDGQLDELLEEIISLYQRA-----AADKDVVIVEGMVPTRHASYAARV 120
            P+P A +ER+L   +LD L+E++I L+ +A         D+++VEG+VPT H +YA ++
Sbjct: 75  APIPQADMERLLRQDRLDVLMEQVIELFDQAMDGHDGTTPDLIVVEGVVPTAHGTYATQL 134

Query: 121 NFHLAKSLDAEVILVSAPENETLTELTDRIEIQAQLFGGPRDPKVLGVILNKVRG----- 175
           N  LA +L+A VILV + +      L +++++ A  FGG    + LG IL +++      
Sbjct: 135 NAQLAHALNARVILVGSGDAAAPEALAEQLDMHASAFGGVGSARTLGCILMRMQNLPGGE 194

Query: 176 EADAANAEDGVA---DFARRLTEHSPLLRDD-FRLIGCIPWQDELNAARTRDIADLLSAR 231
           E   A     V     F   L  HSP L  D F LIG +P+   L A R  D+A  L AR
Sbjct: 195 EPTLAPGTSSVMLDDTFLDELRRHSPALATDRFHLIGVVPYNPALIAPRVVDVARALDAR 254

Query: 232 VINAGDYEQRRVQKIVLCARAVPNTVQLLKPGVLVVTPGDRDDIILAASLAAMNGVPLAG 291
            ++ GD   RRV    LCAR+  N + + +PG L+VT GDRDDI+LA++LA MNGVP+AG
Sbjct: 255 FLHEGDAANRRVLSTSLCARSAANALHVFRPGSLIVTSGDRDDIVLASALATMNGVPMAG 314

Query: 292 LLLCSDFPPDPRIMELCRGALQGGLPVLSVATGSYDTATNLNRMNKEIPVDDRERAERVT 351
           +LL + F P+  ++E+CR AL+ G+PVL+V T S+ TA NL RM  +IP+DD ERAE+VT
Sbjct: 315 VLLTNGFMPNDNMIEMCRPALKTGMPVLAVDTDSFTTAKNLGRMGNDIPMDDLERAEQVT 374

Query: 352 EFVAGHIDFEWLKQRCGTPRELRLSPPAFRYQVVQRAQKAGKRIVLPEGSEPRTVQAAAI 411
            FVAGH+D +WLK         RLSP AFR+Q+V+ AQ+A +RI+LPEGSEPRTV+AAAI
Sbjct: 375 RFVAGHLDLQWLKDHLSRGFTRRLSPSAFRHQLVKLAQRANRRIILPEGSEPRTVEAAAI 434

Query: 412 CQARGIARCVLLAKPEEVQAVAQAQGIVLPEGLEIIDPDLVRQRYVEPMVELRKGKGLNA 471
           CQ RGIA CVLLA+ EEV+ VA+ +GI LPEGLEI+DP+ +R RYV PMVE R+GK +N 
Sbjct: 435 CQRRGIANCVLLARREEVEEVARNRGIELPEGLEILDPEHIRSRYVAPMVERRRGK-VNE 493

Query: 472 PMAEQQLEDSVVLATMMLALDEVDGLVSGAIHTTASTIRPALQLIKTAPGYNLVSSVFFM 531
             AE QL+D+VVL TMML LDEVDGLVSGAIHTTA+T+RPA QLIKTAPGY  VSS+FFM
Sbjct: 494 LTAEDQLQDNVVLGTMMLQLDEVDGLVSGAIHTTANTVRPAFQLIKTAPGYRQVSSIFFM 553

Query: 532 LLPDQVLVYGDCAVNPDPSASDLAEIAVQSAASAQAFGIPARVAMISYSTGDSGSGVDVD 591
           LLP+QV+VYGDCAVNPDP A  LAEIA+QSA SAQAFGI  RVAMISYSTG+SGSG DVD
Sbjct: 554 LLPEQVVVYGDCAVNPDPDAEALAEIAIQSARSAQAFGIEPRVAMISYSTGESGSGADVD 613

Query: 592 KVREATRLAREQRPDLLIDGPLQYDAAAIASVGRQKAPNSPVAGQATVFIFPDLNTGNTT 651
           KVR+ATRLAREQ PDLLIDGPLQYDAAAI SVGRQKAP+SPVAG+ATVF+FPDLNTGNTT
Sbjct: 614 KVRQATRLAREQAPDLLIDGPLQYDAAAIESVGRQKAPDSPVAGRATVFVFPDLNTGNTT 673

Query: 652 YKAVQRSADCVSVGPMLQGLRKPVNDLSRGALVEDIVYTIALTAIQA 698
           YKAVQRSA  VSVGPMLQGL KPVNDLSRGALV+DIVYTIALTAIQA
Sbjct: 674 YKAVQRSARVVSVGPMLQGLNKPVNDLSRGALVDDIVYTIALTAIQA 720


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: 1360
Number of extensions: 55
Number of successful extensions: 4
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: 724
Length adjustment: 39
Effective length of query: 665
Effective length of database: 685
Effective search space:   455525
Effective search space used:   455525
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: 55 (25.8 bits)

Align candidate WP_086512002.1 BZY95_RS21875 (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.12226.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-126  408.5   0.0   1.4e-126  408.1   0.0    1.1  1  lcl|NCBI__GCF_002151265.1:WP_086512002.1  BZY95_RS21875 phosphate acetyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086512002.1  BZY95_RS21875 phosphate acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.1   0.0  1.4e-126  1.4e-126       1     304 []     418     717 ..     418     717 .. 0.97

  Alignments for each domain:
  == domain 1  score: 408.1 bits;  conditional E-value: 1.4e-126
                                 TIGR00651   1 ivlPEgseervlkAaallaekkiaekvllvnkeeevkn.kakevnlklgkvvvedpdvskdiekyverl 68 
                                               i+lPEgse+r+++Aaa++++++ia++vll++ ee++++ + ++++l  g  ++++++++    +yv  +
  lcl|NCBI__GCF_002151265.1:WP_086512002.1 418 IILPEGSEPRTVEAAAICQRRGIANCVLLARREEVEEVaRNRGIELPEGLEILDPEHIR---SRYVAPM 483
                                               8*********************************9998667778887776666666666...9****** PP

                                 TIGR00651  69 yekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvf 137
                                               +e+r+ k v+e +a++ql+D+v+l++++++l+e+dglvsGa +tta+t+rpa+q+ikt++g + vss+f
  lcl|NCBI__GCF_002151265.1:WP_086512002.1 484 VERRRGK-VNELTAEDQLQDNVVLGTMMLQLDEVDGLVSGAIHTTANTVRPAFQLIKTAPGYRQVSSIF 551
                                               *******.************************************************************* PP

                                 TIGR00651 138 imekeeevlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvkeAv 206
                                               +m ++e+v+v++DCav++dP+ae LAeiA+qsa sa+++g +ep+va++syst+ sg+g++v+kv++A+
  lcl|NCBI__GCF_002151265.1:WP_086512002.1 552 FMLLPEQVVVYGDCAVNPDPDAEALAEIAIQSARSAQAFG-IEPRVAMISYSTGESGSGADVDKVRQAT 619
                                               ****************************************.**************************** PP

                                 TIGR00651 207 kilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiGP 275
                                               ++++e++pdll+dG+lq+DaA +e+v ++kap+s+vag+a+vfvFPdL++Gn++Yk+vqR+a + ++GP
  lcl|NCBI__GCF_002151265.1:WP_086512002.1 620 RLAREQAPDLLIDGPLQYDAAAIESVGRQKAPDSPVAGRATVFVFPDLNTGNTTYKAVQRSARVVSVGP 688
                                               ********************************************************************* PP

                                 TIGR00651 276 ilqGlakPvnDLsRGasvedivnvviita 304
                                               +lqGl+kPvnDLsRGa+v+div+++++ta
  lcl|NCBI__GCF_002151265.1:WP_086512002.1 689 MLQGLNKPVNDLSRGALVDDIVYTIALTA 717
                                               ***************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (304 nodes)
Target sequences:                          1  (724 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 19.06
//
[ok]

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

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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