Alignments for a candidate for hmgA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Herbaspirillum seropedicae SmR1

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate HSERO_RS05605 HSERO_RS05605 homogentisate 1,2-dioxygenase

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



>FitnessBrowser__HerbieS:HSERO_RS05605
          Length = 445

 Score =  690 bits (1780), Expect = 0.0
 Identities = 323/428 (75%), Positives = 357/428 (83%), Gaps = 1/428 (0%)

Query: 20  TPGYQSGFANEFATEALPGALPVGQNSPQRAPYGLYAEQISGTAFTAPRAHNRRSWCYRI 79
           T GYQSGF NEFATEALP ALP  QNSPQR  YGLYAEQISGTAFTAPR HNRRSW YRI
Sbjct: 15  TRGYQSGFGNEFATEALPSALPAHQNSPQRVAYGLYAEQISGTAFTAPRGHNRRSWLYRI 74

Query: 80  RAAAMHEPFTRVEQSRIVSHFDAVPPSPNQMRWSPPAMPKEPTDFVDGIITMAGNGGPEA 139
           R AAMH PF  + Q  +VS FD V P PNQ+RW P  MP  PTDF+DG++TMAGNG P+A
Sbjct: 75  RPAAMHHPFEAMSQGLLVSRFDDVAPPPNQLRWDPLPMPTTPTDFIDGLVTMAGNGSPQA 134

Query: 140 MSGCGIHLYLANRSMTDRFFYNADGEMLIVPQQGRLRLATEMGLLDVEPQEIVVIPRGVR 199
            SGC IHLY AN SMTDRFFY+ADGE+LIVPQ GRL+L TEMG++D+EPQEI VIPRGVR
Sbjct: 135 QSGCAIHLYAANCSMTDRFFYSADGELLIVPQMGRLQLRTEMGVIDIEPQEIAVIPRGVR 194

Query: 200 FRVELPDGEARGYICENYGALFRLPDLGVIGSNGLANPRDFLTPHAWYEDREGDFELVAK 259
           F+V LP GEARGYICEN+GAL RLPDLG +GSNGLANPRDF TPHAWYEDREGDF+L+AK
Sbjct: 195 FQVRLPGGEARGYICENFGALLRLPDLGPLGSNGLANPRDFATPHAWYEDREGDFQLIAK 254

Query: 260 FQGNLWRAAIGHSPLDVVAWHGNYAPYKYDLRRFNTIGSISFDHPDPSIFLVLQSPSDTP 319
           F G LW+A IGHSPLDVVAWHGNYAPYKYDLR FNTIGSIS+DHPDPSIFLVLQS SDTP
Sbjct: 255 FGGQLWQARIGHSPLDVVAWHGNYAPYKYDLRHFNTIGSISYDHPDPSIFLVLQSQSDTP 314

Query: 320 GVDSIDFVIFGPRWLAMQNTFRPPWFHRNIASEFMGLIEGVYDAK-ADGFSPGGASLHNC 378
           GVD+IDFVIF PRWLA +NTFRPPWFHRN+ASE+MGLI G YDAK   GF PGG SLHNC
Sbjct: 315 GVDTIDFVIFPPRWLAAENTFRPPWFHRNVASEYMGLITGQYDAKEGGGFVPGGGSLHNC 374

Query: 379 MSGHGPDAETFAKATAADTSQPHRIGDTMAFMFETPAVIRPTPYAAESAQLQDDYYRCWQ 438
           MSGHGPDA TF KA+  DTS P+++  TMAFMFET  ++ PT +A  S  LQ DY  CW 
Sbjct: 375 MSGHGPDAATFEKASRIDTSTPNKVDHTMAFMFETRNILCPTRHALASPALQRDYQDCWL 434

Query: 439 GLKKHFNP 446
           G++K+FNP
Sbjct: 435 GIQKNFNP 442


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: 842
Number of extensions: 33
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: 445
Length adjustment: 33
Effective length of query: 416
Effective length of database: 412
Effective search space:   171392
Effective search space used:   171392
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 HSERO_RS05605 HSERO_RS05605 (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.18360.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   4.7e-205  667.2   0.0   5.4e-205  667.0   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS05605  HSERO_RS05605 homogentisate 1,2-


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS05605  HSERO_RS05605 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  667.0   0.0  5.4e-205  5.4e-205       3     429 .]      17     440 ..      15     440 .. 0.98

  Alignments for each domain:
  == domain 1  score: 667.0 bits;  conditional E-value: 5.4e-205
                                  TIGR01015   3 kylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafe 70 
                                                 y+sGfgnef++ea+p alP  qnsPq+++yglyaeq+sG+aftaPr +n+rswlyrirP+a+h++fe
  lcl|FitnessBrowser__HerbieS:HSERO_RS05605  17 GYQSGFGNEFATEALPSALPAHQNSPQRVAYGLYAEQISGTAFTAPRGHNRRSWLYRIRPAAMHHPFE 84 
                                                6******************************************************************* PP

                                  TIGR01015  71 elkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasm 138
                                                +++  +  l++ f+++a+ pnqlrw+pl++p+   +df++glvt+ag+g +++++G a+hlya+n sm
  lcl|FitnessBrowser__HerbieS:HSERO_RS05605  85 AMS--QGLLVSRFDDVAPPPNQLRWDPLPMPT-TPTDFIDGLVTMAGNGSPQAQSGCAIHLYAANCSM 149
                                                *99..89************************7.99********************************* PP

                                  TIGR01015 139 edevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfq 205
                                                +d+ fy+adG+llivpq+G l+++te+G++++eP+eiaviprGvrf+v +  +earGyi+e++ga  +
  lcl|FitnessBrowser__HerbieS:HSERO_RS05605 150 TDRFFYSADGELLIVPQMGRLQLRTEMGVIDIEPQEIAVIPRGVRFQVRLPgGEARGYICENFGALLR 217
                                                ***************************************************999************** PP

                                  TIGR01015 206 lPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPyky 273
                                                lPdlGP+G+nglanprdf +P a++ed+e+  ++++i kf g+l++a+++hspldvvawhGny+Pyky
  lcl|FitnessBrowser__HerbieS:HSERO_RS05605 218 LPDLGPLGSNGLANPRDFATPHAWYEDREG--DFQLIAKFGGQLWQARIGHSPLDVVAWHGNYAPYKY 283
                                                ******************************..9*********************************** PP

                                  TIGR01015 274 dlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGl 341
                                                dl++fn+i+s+s+dhpdPsif vl ++sd++G+ ++dfvifpPrwl ae+tfrPP++hrnv se+mGl
  lcl|FitnessBrowser__HerbieS:HSERO_RS05605 284 DLRHFNTIGSISYDHPDPSIFLVLQSQSDTPGVDTIDFVIFPPRWLAAENTFRPPWFHRNVASEYMGL 351
                                                ******************************************************************** PP

                                  TIGR01015 342 ikGkydakeeG.fvpgGaslhnimsahGPdveafekasnael.kPekiddgtlafmfesslslavtkl 407
                                                i+G+ydake+G fvpgG+slhn+ms hGPd+++fekas+ +  +P+k+d+ t+afmfe++  l  t++
  lcl|FitnessBrowser__HerbieS:HSERO_RS05605 352 ITGQYDAKEGGgFVPGGGSLHNCMSGHGPDAATFEKASRIDTsTPNKVDH-TMAFMFETRNILCPTRH 418
                                                *********877***************************98637*****9.***************** PP

                                  TIGR01015 408 akelekldedyeevwqglkkkf 429
                                                a  + +l++dy+++w g++k+f
  lcl|FitnessBrowser__HerbieS:HSERO_RS05605 419 ALASPALQRDYQDCWLGIQKNF 440
                                                *******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (445 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.75
//
[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