Alignments for a candidate for hmgA in Paraburkholderia sp. CCGE1002

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Paraburkholderia sp. CCGE1002

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate WP_013088540.1 BC1002_RS02705 homogentisate 1,2-dioxygenase

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



>NCBI__GCF_000092885.1:WP_013088540.1
          Length = 448

 Score =  722 bits (1864), Expect = 0.0
 Identities = 339/430 (78%), Positives = 374/430 (86%), Gaps = 1/430 (0%)

Query: 21  PGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRIR 80
           PGYQSGFANEFATEALPGALP G+NSPQRA YGLYAEQISGTAFTAPR HNRRSW YRIR
Sbjct: 19  PGYQSGFANEFATEALPGALPTGRNSPQRAAYGLYAEQISGTAFTAPRGHNRRSWLYRIR 78

Query: 81  AAAMHEPFTRVEQSRIVSHFDAVPPSP-NQMRWSPPAMPKEPTDFVDGIITMAGNGGPEA 139
            AAMH+PFT +   R+V++F  VPP+P NQ+RW P  MP EPTDF+DG +TMAGNG  EA
Sbjct: 79  PAAMHKPFTLMPSERLVANFAEVPPTPPNQLRWDPLPMPSEPTDFIDGWVTMAGNGSAEA 138

Query: 140 MSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVR 199
           MSGC IHLY ANRSM +RFFY+ADGE+LIVPQQGRL +ATEMG +D+EP EI VIPRGVR
Sbjct: 139 MSGCAIHLYAANRSMHERFFYSADGELLIVPQQGRLHIATEMGRIDIEPFEIAVIPRGVR 198

Query: 200 FRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDFLTPHAWYEDREGDFELVAK 259
           F V LPDG ARGYICEN+GAL RLP+LG IGSNGLANPRDFLTPHA YEDREG FELVAK
Sbjct: 199 FAVSLPDGSARGYICENFGALLRLPELGPIGSNGLANPRDFLTPHAAYEDREGAFELVAK 258

Query: 260 FQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSPSDTP 319
             G LWRA IGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQS SDTP
Sbjct: 259 MNGKLWRADIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSQSDTP 318

Query: 320 GVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVYDAKADGFSPGGASLHNCM 379
           GVD++DFVIF PRWLA ++TFRPPWFHRN+ASEFMGL+ GVYDAKA+GF PGGASLHNCM
Sbjct: 319 GVDTLDFVIFPPRWLAAEDTFRPPWFHRNVASEFMGLVHGVYDAKAEGFVPGGASLHNCM 378

Query: 380 SGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPTPYAAESAQLQDDYYRCWQG 439
           +GHGPDA+TF KA+  DTS P ++ DTMAFMFET  +I+PT +A ESAQLQ  YY CWQG
Sbjct: 379 TGHGPDADTFEKASHIDTSVPKKVDDTMAFMFETRTLIKPTRFALESAQLQAHYYECWQG 438

Query: 440 LKKHFNPNER 449
           L+KHFNP +R
Sbjct: 439 LEKHFNPEQR 448


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: 835
Number of extensions: 24
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: 448
Length adjustment: 33
Effective length of query: 416
Effective length of database: 415
Effective search space:   172640
Effective search space used:   172640
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 WP_013088540.1 BC1002_RS02705 (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.14885.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.9e-206  670.7   0.0   4.5e-206  670.5   0.0    1.0  1  lcl|NCBI__GCF_000092885.1:WP_013088540.1  BC1002_RS02705 homogentisate 1,2


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013088540.1  BC1002_RS02705 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  670.5   0.0  4.5e-206  4.5e-206       3     429 .]      20     443 ..      18     443 .. 0.98

  Alignments for each domain:
  == domain 1  score: 670.5 bits;  conditional E-value: 4.5e-206
                                 TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafee 71 
                                                y+sGf nef++ea+pgalP+G+nsPq+a+yglyaeq+sG+aftaPr +n+rswlyrirP+a+h++f+ 
  lcl|NCBI__GCF_000092885.1:WP_013088540.1  20 GYQSGFANEFATEALPGALPTGRNSPQRAAYGLYAEQISGTAFTAPRGHNRRSWLYRIRPAAMHKPFTL 88 
                                               6******************************************************************99 PP

                                 TIGR01015  72 lkeseekltanfkeeas.dpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasme 139
                                               +   +e l+anf e+++  pnqlrw+pl++ps e +df++g vt+ag+g a++ +G a+hlya+n sm+
  lcl|NCBI__GCF_000092885.1:WP_013088540.1  89 MP--SERLVANFAEVPPtPPNQLRWDPLPMPS-EPTDFIDGWVTMAGNGSAEAMSGCAIHLYAANRSMH 154
                                               99..6889999999988689***********8.99********************************** PP

                                 TIGR01015 140 devfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlP 207
                                               ++ fy+adG+llivpq+G l+i te+Gr+++eP eiaviprGvrf+v++  + arGyi+e++ga  +lP
  lcl|NCBI__GCF_000092885.1:WP_013088540.1 155 ERFFYSADGELLIVPQQGRLHIATEMGRIDIEPFEIAVIPRGVRFAVSLPdGSARGYICENFGALLRLP 223
                                               *************************************************9889**************** PP

                                 TIGR01015 208 dlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlk 276
                                               +lGPiG+nglanprdf +P aa+ed+e+   ++++ k +gkl+ a ++hspldvvawhGny+Pykydl+
  lcl|NCBI__GCF_000092885.1:WP_013088540.1 224 ELGPIGSNGLANPRDFLTPHAAYEDREG--AFELVAKMNGKLWRADIGHSPLDVVAWHGNYAPYKYDLR 290
                                               ****************************..89************************************* PP

                                 TIGR01015 277 kfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGk 345
                                               +fn+i+s+sfdhpdPsif vl ++sd++G+ + dfvifpPrwl ae+tfrPP++hrnv sefmGl++G 
  lcl|NCBI__GCF_000092885.1:WP_013088540.1 291 RFNTIGSISFDHPDPSIFLVLQSQSDTPGVDTLDFVIFPPRWLAAEDTFRPPWFHRNVASEFMGLVHGV 359
                                               ********************************************************************* PP

                                 TIGR01015 346 ydakeeGfvpgGaslhnimsahGPdveafekasnael.kPekiddgtlafmfesslslavtklakelek 413
                                               ydak+eGfvpgGaslhn+m+ hGPd+++fekas+ +   P+k+dd t+afmfe++  ++ t++a e+++
  lcl|NCBI__GCF_000092885.1:WP_013088540.1 360 YDAKAEGFVPGGASLHNCMTGHGPDADTFEKASHIDTsVPKKVDD-TMAFMFETRTLIKPTRFALESAQ 427
                                               **********************************98636******.*********************** PP

                                 TIGR01015 414 ldedyeevwqglkkkf 429
                                               l+++y+e+wqgl+k+f
  lcl|NCBI__GCF_000092885.1:WP_013088540.1 428 LQAHYYECWQGLEKHF 443
                                               **************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (448 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 8.05
//
[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