Alignments for a candidate for hmgA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Dyella japonica UNC79MFTsu3.2

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate N515DRAFT_0361 N515DRAFT_0361 homogentisate 1,2-dioxygenase

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



>FitnessBrowser__Dyella79:N515DRAFT_0361
          Length = 430

 Score =  652 bits (1682), Expect = 0.0
 Identities = 302/425 (71%), Positives = 345/425 (81%)

Query: 20  TPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRI 79
           T GYQSGF NEFATEA+ G LP GQNSPQR  +GLYAEQ+SG+AFTAPR  NRRSW YRI
Sbjct: 3   TKGYQSGFGNEFATEAVAGVLPHGQNSPQRVAHGLYAEQLSGSAFTAPRHSNRRSWLYRI 62

Query: 80  RAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKEPTDFVDGIITMAGNGGPEA 139
           R AA+H PF         + FD  P +PNQ+RW P  +P  PTDFVDG++T+AGNGGP  
Sbjct: 63  RPAAVHRPFEPRAHEHFHNRFDEAPATPNQLRWDPWPLPARPTDFVDGLVTLAGNGGPAE 122

Query: 140 MSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVR 199
            +GCGIH+Y ANRSM  RFFY+ADGE+L+VPQQGRLR+ TE+G+LDV P EI VIPRGVR
Sbjct: 123 QAGCGIHIYAANRSMLGRFFYDADGELLLVPQQGRLRVCTELGVLDVAPLEIAVIPRGVR 182

Query: 200 FRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDFLTPHAWYEDREGDFELVAK 259
           FRVEL DGEARGY+CEN+GAL RLPDLG IG+N +A PRDFLTP AWYED EGDFEL+AK
Sbjct: 183 FRVELIDGEARGYVCENFGALLRLPDLGPIGANSMALPRDFLTPQAWYEDVEGDFELIAK 242

Query: 260 FQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSPSDTP 319
           FQG+LW AAI HSPLDVVAWHGNYAPYKYDL  +NT+GSIS DHPDPSIF VL SPSDTP
Sbjct: 243 FQGSLWTAAIDHSPLDVVAWHGNYAPYKYDLTTYNTVGSISVDHPDPSIFTVLTSPSDTP 302

Query: 320 GVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVYDAKADGFSPGGASLHNCM 379
           G  ++DFVIF PRWL  ++TFRPP+FHRN+ASEFMGLI+G YDAK  GF PGGASLHNCM
Sbjct: 303 GTANVDFVIFPPRWLVAEHTFRPPYFHRNVASEFMGLIQGAYDAKEGGFVPGGASLHNCM 362

Query: 380 SGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPTPYAAESAQLQDDYYRCWQG 439
           SGHGPDA +F KA+ AD S+P  +  TMAFMFET  VIRPT  A ++ QLQ  YY CWQG
Sbjct: 363 SGHGPDAASFEKASGADVSKPDHLTGTMAFMFETRKVIRPTRQALDAPQLQGSYYECWQG 422

Query: 440 LKKHF 444
           ++KHF
Sbjct: 423 IRKHF 427


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: 803
Number of extensions: 27
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: 449
Length of database: 430
Length adjustment: 32
Effective length of query: 417
Effective length of database: 398
Effective search space:   165966
Effective search space used:   165966
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 N515DRAFT_0361 N515DRAFT_0361 (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.9770.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.4e-208  677.5   0.0     4e-208  677.3   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0361  N515DRAFT_0361 homogentisate 1,2


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0361  N515DRAFT_0361 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  677.3   0.0    4e-208    4e-208       3     429 .]       5     427 ..       3     427 .. 0.98

  Alignments for each domain:
  == domain 1  score: 677.3 bits;  conditional E-value: 4e-208
                                    TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaahea 68 
                                                   y+sGfgnef++eav+g lP+GqnsPq++++glyaeqlsGsaftaPr++n+rswlyrirP+a h++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0361   5 GYQSGFGNEFATEAVAGVLPHGQNSPQRVAHGLYAEQLSGSAFTAPRHSNRRSWLYRIRPAAVHRP 70 
                                                  6***************************************************************** PP

                                    TIGR01015  69 feelkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyav 134
                                                  fe+++  +e++ + f+e +++pnqlrw+p ++p+ + +dfv+glvtlag+g ++++aG ++h+ya+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0361  71 FEPRA--HEHFHNRFDEAPATPNQLRWDPWPLPA-RPTDFVDGLVTLAGNGGPAEQAGCGIHIYAA 133
                                                  ***99..7999**********************6.9****************************** PP

                                    TIGR01015 135 nasmedevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilev 199
                                                  n sm  + fy+adG+ll+vpq+G l++ telG+l+v+P eiaviprGvrfrve+  +earGy++e+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0361 134 NRSMLGRFFYDADGELLLVPQQGRLRVCTELGVLDVAPLEIAVIPRGVRFRVELIdGEARGYVCEN 199
                                                  *****************************************************9889********* PP

                                    TIGR01015 200 ygakfqlPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawh 265
                                                  +ga  +lPdlGPiGan++a prdf +P a++ed e+  ++++i kfqg+l++a +dhspldvvawh
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0361 200 FGALLRLPDLGPIGANSMALPRDFLTPQAWYEDVEG--DFELIAKFQGSLWTAAIDHSPLDVVAWH 263
                                                  **********************************99..9*************************** PP

                                    TIGR01015 266 GnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyh 331
                                                  Gny+Pykydl+++n+++s+s dhpdPsiftvlt+psd++Gta++dfvifpPrwlvae+tfrPPy+h
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0361 264 GNYAPYKYDLTTYNTVGSISVDHPDPSIFTVLTSPSDTPGTANVDFVIFPPRWLVAEHTFRPPYFH 329
                                                  ****************************************************************** PP

                                    TIGR01015 332 rnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasnael.kPekiddgtlafmf 396
                                                  rnv sefmGli+G+ydake+GfvpgGaslhn+ms hGPd+++fekas a++ kP+++   t+afmf
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0361 330 RNVASEFMGLIQGAYDAKEGGFVPGGASLHNCMSGHGPDAASFEKASGADVsKPDHLTG-TMAFMF 394
                                                  *************************************************9846888876.****** PP

                                    TIGR01015 397 esslslavtklakelekldedyeevwqglkkkf 429
                                                  e++ +++ t++a  + +l+  y+e+wqg++k+f
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0361 395 ETRKVIRPTRQALDAPQLQGSYYECWQGIRKHF 427
                                                  *******************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (430 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: 9.59
//
[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