Alignments for a candidate for hmgA in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Burkholderia phytofirmans PsJN

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate BPHYT_RS03800 BPHYT_RS03800 homogentisate 1,2-dioxygenase

Query= reanno::Cup4G11:RR42_RS31275
         (449 letters)



>FitnessBrowser__BFirm:BPHYT_RS03800
          Length = 432

 Score =  719 bits (1856), Expect = 0.0
 Identities = 339/430 (78%), Positives = 372/430 (86%), Gaps = 1/430 (0%)

Query: 21  PGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRIR 80
           PGYQSGFANEFATEALPGALP G+NSPQRA YGLYAEQ+SGTAFTAPR HNRRSW YRIR
Sbjct: 3   PGYQSGFANEFATEALPGALPQGRNSPQRAAYGLYAEQLSGTAFTAPRGHNRRSWLYRIR 62

Query: 81  AAAMHEPFTRVEQSRIVSHFDAVPPSP-NQMRWSPPAMPKEPTDFVDGIITMAGNGGPEA 139
            AA+H PFT +   R+V++F  VPP+P NQ+RW    MP EPTDF+DG +TMAGNG  E+
Sbjct: 63  PAAVHMPFTPLPSERLVANFAEVPPTPPNQLRWDALPMPAEPTDFIDGWVTMAGNGAAES 122

Query: 140 MSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVR 199
           M+GC IH+Y ANRSM DRFFY ADGE+LIVPQ+GRL +ATE G LDV P EI VIPRGVR
Sbjct: 123 MTGCAIHVYAANRSMQDRFFYTADGELLIVPQEGRLHIATEFGKLDVGPFEIAVIPRGVR 182

Query: 200 FRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDFLTPHAWYEDREGDFELVAK 259
           F V LPDG ARGYICEN+GAL RLPDLG IGSNGLANPRDFLTPHA YEDREGDFELVAK
Sbjct: 183 FAVSLPDGVARGYICENFGALLRLPDLGPIGSNGLANPRDFLTPHAAYEDREGDFELVAK 242

Query: 260 FQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSPSDTP 319
             GNLWRA IGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQS +DTP
Sbjct: 243 MNGNLWRADIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSQTDTP 302

Query: 320 GVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVYDAKADGFSPGGASLHNCM 379
           GVDSIDFVIF PRWLA ++TFRPPWFHRN+ASEFMGL+ GVYDAKA+GF PGGASLHNCM
Sbjct: 303 GVDSIDFVIFPPRWLAAEDTFRPPWFHRNVASEFMGLVHGVYDAKAEGFVPGGASLHNCM 362

Query: 380 SGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPTPYAAESAQLQDDYYRCWQG 439
           SGHGPDAETF KA+ +DTS P ++GDTMAFMFET  +I+PT +A E+AQLQ  YY CWQG
Sbjct: 363 SGHGPDAETFEKASHSDTSTPKKVGDTMAFMFETRTLIKPTRFALETAQLQAHYYECWQG 422

Query: 440 LKKHFNPNER 449
           L KHFNP +R
Sbjct: 423 LTKHFNPEQR 432


Lambda     K      H
   0.320    0.138    0.439 

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: 838
Number of extensions: 26
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: 449
Length of database: 432
Length adjustment: 32
Effective length of query: 417
Effective length of database: 400
Effective search space:   166800
Effective search space used:   166800
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: 51 (24.3 bits)

Align candidate BPHYT_RS03800 BPHYT_RS03800 (homogentisate 1,2-dioxygenase)
to HMM TIGR01015 (hmgA: homogentisate 1,2-dioxygenase (EC 1.13.11.5))

# 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/TIGR01015.hmm
# target sequence database:        /tmp/gapView.18641.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01015  [M=429]
Accession:   TIGR01015
Description: hmgA: homogentisate 1,2-dioxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.3e-204  665.7   0.0   1.4e-204  665.6   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS03800  BPHYT_RS03800 homogentisate 1,2-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS03800  BPHYT_RS03800 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  665.6   0.0  1.4e-204  1.4e-204       3     429 .]       4     427 ..       2     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 665.6 bits;  conditional E-value: 1.4e-204
                                TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafeel 72 
                                               y+sGf nef++ea+pgalP+G+nsPq+a+yglyaeqlsG+aftaPr +n+rswlyrirP+a h +f++l
  lcl|FitnessBrowser__BFirm:BPHYT_RS03800   4 GYQSGFANEFATEALPGALPQGRNSPQRAAYGLYAEQLSGTAFTAPRGHNRRSWLYRIRPAAVHMPFTPL 73 
                                              6********************************************************************9 PP

                                TIGR01015  73 keseekltanfkeeas.dpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmede 141
                                                 +e l+anf e+++  pnqlrw+ l++p+ e +df++g vt+ag+g a+s +G a+h+ya+n sm+d+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03800  74 P--SERLVANFAEVPPtPPNQLRWDALPMPA-EPTDFIDGWVTMAGNGAAESMTGCAIHVYAANRSMQDR 140
                                              9..6889999999988689***********6.9************************************* PP

                                TIGR01015 142 vfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPdlG 210
                                               fy adG+llivpq+G l+i te+G+l+v P eiaviprGvrf+v++  + arGyi+e++ga  +lPdlG
  lcl|FitnessBrowser__BFirm:BPHYT_RS03800 141 FFYTADGELLIVPQEGRLHIATEFGKLDVGPFEIAVIPRGVRFAVSLPdGVARGYICENFGALLRLPDLG 210
                                              ***********************************************9778******************* PP

                                TIGR01015 211 PiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkkfnv 280
                                              PiG+nglanprdf +P aa+ed+e+  +++++ k +g+l+ a ++hspldvvawhGny+Pykydl++fn+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03800 211 PIGSNGLANPRDFLTPHAAYEDREG--DFELVAKMNGNLWRADIGHSPLDVVAWHGNYAPYKYDLRRFNT 278
                                              *************************..9****************************************** PP

                                TIGR01015 281 insvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGkydake 350
                                              i+s+sfdhpdPsif vl +++d++G+  +dfvifpPrwl ae+tfrPP++hrnv sefmGl++G ydak+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03800 279 IGSISFDHPDPSIFLVLQSQTDTPGVDSIDFVIFPPRWLAAEDTFRPPWFHRNVASEFMGLVHGVYDAKA 348
                                              ********************************************************************** PP

                                TIGR01015 351 eGfvpgGaslhnimsahGPdveafekasnael.kPekiddgtlafmfesslslavtklakelekldedye 419
                                              eGfvpgGaslhn+ms hGPd+e+fekas+++  +P+k++d t+afmfe++  ++ t++a e+++l+++y+
  lcl|FitnessBrowser__BFirm:BPHYT_RS03800 349 EGFVPGGASLHNCMSGHGPDAETFEKASHSDTsTPKKVGD-TMAFMFETRTLIKPTRFALETAQLQAHYY 417
                                              ****************************9986379*****.***************************** PP

                                TIGR01015 420 evwqglkkkf 429
                                              e+wqgl k+f
  lcl|FitnessBrowser__BFirm:BPHYT_RS03800 418 ECWQGLTKHF 427
                                              ********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (432 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.43
//
[ok]

This GapMind analysis is from Sep 17 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