Alignments for a candidate for hmgA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Halomonas desiderata SP1

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate WP_086509181.1 BZY95_RS06625 homogentisate 1,2-dioxygenase

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



>NCBI__GCF_002151265.1:WP_086509181.1
          Length = 436

 Score =  561 bits (1446), Expect = e-164
 Identities = 271/429 (63%), Positives = 326/429 (75%), Gaps = 4/429 (0%)

Query: 23  YQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRIRAA 82
           YQSGF N FA+EALPGALP GQNSPQ+  YGLYAEQ++G+AFTAPR  N RSW YRIR +
Sbjct: 8   YQSGFRNHFASEALPGALPAGQNSPQKCAYGLYAEQLTGSAFTAPRHANLRSWLYRIRPS 67

Query: 83  AMHEPFTRVEQSRIVSHFDAVPPS-PNQMRWSPPAMPKEPTDFVDGIITMAGNGGPEAMS 141
            +   +T +E  R+ +   A P + PNQMRW P  +P EPTDFVDG++T+A NG     +
Sbjct: 68  VVQSAYTPLENGRVATSPLARPAADPNQMRWDPLPIPAEPTDFVDGLLTIAVNGDAGTQA 127

Query: 142 GCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVRFR 201
           GCG+H+Y  NR MT+RFFY+ADGE+LIVPQQG LRL TE+G L+V+  EI VIPRG++F+
Sbjct: 128 GCGVHVYAFNRDMTERFFYDADGELLIVPQQGTLRLRTELGELEVKGGEIAVIPRGMKFQ 187

Query: 202 VELPDGE--ARGYICENYGALFRLPDLGVIGSNGLANPRDFLTPHAWYEDREGDFELVAK 259
           V L +G   ARGY+CENYG+   LP LG IG+NGLANPRDF +P A +ED EGDFELVAK
Sbjct: 188 VRLAEGSDAARGYVCENYGSPLELPGLGPIGANGLANPRDFESPVAAFEDIEGDFELVAK 247

Query: 260 FQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSPSDTP 319
           F G  W   +GHSPLDVVAWHGNYAPYKYDL +FNTI ++SFDHPDPSIF VL SPSDTP
Sbjct: 248 FSGRFWVTKLGHSPLDVVAWHGNYAPYKYDLAKFNTINTVSFDHPDPSIFTVLTSPSDTP 307

Query: 320 GVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVYDAKADGFSPGGASLHNCM 379
           G+ +IDFVIF PRW+  +NTFRPP+FHRN+ SEFMGLI G YDAKA+GF PGGASLHN M
Sbjct: 308 GMANIDFVIFPPRWMVAENTFRPPYFHRNLMSEFMGLIHGEYDAKAEGFLPGGASLHNSM 367

Query: 380 SGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPTPYAAESAQLQDDYYRCWQG 439
           S HGPDAETF KA+ A+ + P R+  T+AFMFE+  V  PT  A  +   Q DY   W  
Sbjct: 368 SPHGPDAETFEKASNAELT-PQRLDATLAFMFESRYVYHPTEAALNADIRQRDYVDVWST 426

Query: 440 LKKHFNPNE 448
           L+ HF+P +
Sbjct: 427 LRSHFDPRQ 435


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: 735
Number of extensions: 29
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: 449
Length of database: 436
Length adjustment: 32
Effective length of query: 417
Effective length of database: 404
Effective search space:   168468
Effective search space used:   168468
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_086509181.1 BZY95_RS06625 (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.428.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-212  692.4   0.0   1.2e-212  692.2   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086509181.1  BZY95_RS06625 homogentisate 1,2-


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509181.1  BZY95_RS06625 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  692.2   0.0  1.2e-212  1.2e-212       2     429 .]       6     431 ..       5     431 .. 0.98

  Alignments for each domain:
  == domain 1  score: 692.2 bits;  conditional E-value: 1.2e-212
                                 TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafe 70 
                                               l+y+sGf n+f+sea+pgalP GqnsPqk++yglyaeql+GsaftaPr+ n rswlyrirPs+  +a++
  lcl|NCBI__GCF_002151265.1:WP_086509181.1   6 LEYQSGFRNHFASEALPGALPAGQNSPQKCAYGLYAEQLTGSAFTAPRHANLRSWLYRIRPSVVQSAYT 74 
                                               78****************************************************************999 PP

                                 TIGR01015  71 elkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasme 139
                                               +l+ + ++ t++  + a+dpnq+rw+pl+ip+ e +dfv+gl t+a +gda ++aG +vh+ya+n +m+
  lcl|NCBI__GCF_002151265.1:WP_086509181.1  75 PLE-NGRVATSPLARPAADPNQMRWDPLPIPA-EPTDFVDGLLTIAVNGDAGTQAGCGVHVYAFNRDMT 141
                                               998.799************************6.9*********************************** PP

                                 TIGR01015 140 devfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveveee...arGyilevygakfq 205
                                               ++ fy+adG+llivpq+G+l+++telG+l+v+ +eiaviprG++f+v + e    arGy++e+yg+  +
  lcl|NCBI__GCF_002151265.1:WP_086509181.1 142 ERFFYDADGELLIVPQQGTLRLRTELGELEVKGGEIAVIPRGMKFQVRLAEGsdaARGYVCENYGSPLE 210
                                               ************************************************98432459************* PP

                                 TIGR01015 206 lPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykyd 274
                                               lP lGPiGanglanprdfe Pvaafed e+  +++++ kf+g+++++k +hspldvvawhGny+Pykyd
  lcl|NCBI__GCF_002151265.1:WP_086509181.1 211 LPGLGPIGANGLANPRDFESPVAAFEDIEG--DFELVAKFSGRFWVTKLGHSPLDVVAWHGNYAPYKYD 277
                                               *****************************9..9************************************ PP

                                 TIGR01015 275 lkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlik 343
                                               l kfn+in+vsfdhpdPsiftvlt+psd++G+a++dfvifpPrw+vae+tfrPPy+hrn+msefmGli+
  lcl|NCBI__GCF_002151265.1:WP_086509181.1 278 LAKFNTINTVSFDHPDPSIFTVLTSPSDTPGMANIDFVIFPPRWMVAENTFRPPYFHRNLMSEFMGLIH 346
                                               ********************************************************************* PP

                                 TIGR01015 344 GkydakeeGfvpgGaslhnimsahGPdveafekasnaelkPekiddgtlafmfesslslavtklakele 412
                                               G+ydak+eGf pgGaslhn ms+hGPd+e+fekasnael+P+++d  tlafmfes+++ + t+ a +++
  lcl|NCBI__GCF_002151265.1:WP_086509181.1 347 GEYDAKAEGFLPGGASLHNSMSPHGPDAETFEKASNAELTPQRLDA-TLAFMFESRYVYHPTEAALNAD 414
                                               ********************************************99.********************** PP

                                 TIGR01015 413 kldedyeevwqglkkkf 429
                                                 ++dy +vw++l+++f
  lcl|NCBI__GCF_002151265.1:WP_086509181.1 415 IRQRDYVDVWSTLRSHF 431
                                               **************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (436 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: 10.95
//
[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