Alignments for a candidate for hmgA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Pseudomonas fluorescens FW300-N2E3

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate AO353_15550 AO353_15550 homogentisate 1,2-dioxygenase

Query= reanno::pseudo3_N2E3:AO353_15550
         (434 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_15550
          Length = 434

 Score =  902 bits (2330), Expect = 0.0
 Identities = 434/434 (100%), Positives = 434/434 (100%)

Query: 1   MNLDSTAPALVYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA 60
           MNLDSTAPALVYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA
Sbjct: 1   MNLDSTAPALVYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEA 60

Query: 61  RRTWMYRIQPSANHPAFVKLERQLAGGPLGDVTPNRLRWNPLEIPGEPTDFIDGLVRMAA 120
           RRTWMYRIQPSANHPAFVKLERQLAGGPLGDVTPNRLRWNPLEIPGEPTDFIDGLVRMAA
Sbjct: 61  RRTWMYRIQPSANHPAFVKLERQLAGGPLGDVTPNRLRWNPLEIPGEPTDFIDGLVRMAA 120

Query: 121 NSGSEKPAGISIYHYRANRSMERVFFNADGEWLLVPEQGRLRIATELGVLELEPLEIAVL 180
           NSGSEKPAGISIYHYRANRSMERVFFNADGEWLLVPEQGRLRIATELGVLELEPLEIAVL
Sbjct: 121 NSGSEKPAGISIYHYRANRSMERVFFNADGEWLLVPEQGRLRIATELGVLELEPLEIAVL 180

Query: 181 PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEDLKQPT 240
           PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEDLKQPT
Sbjct: 181 PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEDLKQPT 240

Query: 241 TLVQKFLGELWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300
           TLVQKFLGELWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS
Sbjct: 241 TLVQKFLGELWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300

Query: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGTYDAKAEGFLPGGAS 360
           PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGTYDAKAEGFLPGGAS
Sbjct: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGTYDAKAEGFLPGGAS 360

Query: 361 LHSCMSAHGPDGETCTKAINAELAPSKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDA 420
           LHSCMSAHGPDGETCTKAINAELAPSKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDA
Sbjct: 361 LHSCMSAHGPDGETCTKAINAELAPSKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDA 420

Query: 421 CWASLPVTFNPNRR 434
           CWASLPVTFNPNRR
Sbjct: 421 CWASLPVTFNPNRR 434


Lambda     K      H
   0.320    0.137    0.433 

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: 912
Number of extensions: 25
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: 434
Length of database: 434
Length adjustment: 32
Effective length of query: 402
Effective length of database: 402
Effective search space:   161604
Effective search space used:   161604
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 AO353_15550 AO353_15550 (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.27570.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   5.7e-194  630.6   0.0   6.5e-194  630.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15550  AO353_15550 homogentisate 1,2-di


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_15550  AO353_15550 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  630.5   0.0  6.5e-194  6.5e-194       2     427 ..      10     427 ..       9     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 630.5 bits;  conditional E-value: 6.5e-194
                                     TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaah 66 
                                                   l y+sGfgnef+sea+pgalPvGqnsPqkapygly+e +sG+aft+ r+e +r+w+yri+Psa+h
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15550  10 LVYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEARRTWMYRIQPSANH 74 
                                                   67*************************************************************** PP

                                     TIGR01015  67 eafeelkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhl 131
                                                    af++l+   +    +    +++pn+lrw+pleip+ e +df++glv +a+++  ++ aG++++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15550  75 PAFVKLE--RQLAGGPLG--DVTPNRLRWNPLEIPG-EPTDFIDGLVRMAANSGSEKPAGISIYH 134
                                                   ***9998..455555555..6679***********7.99************************** PP

                                     TIGR01015 132 yavnasmedevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrveveee.arGy 195
                                                   y +n sm ++vf+nadG+ l+vp++G l+i telG+l++eP eiav+prG++fr+e+ ++ arGy
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15550 135 YRANRSM-ERVFFNADGEWLLVPEQGRLRIATELGVLELEPLEIAVLPRGLKFRIELLDPqARGY 198
                                                   *******.89***********************************************96559*** PP

                                     TIGR01015 196 ilevygakfqlPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaakqdhspld 260
                                                   + e++ga  +lPdlGPiG+nglanprdf +Pva +ed +   ++++++kf g+l+ ++ dhspl+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15550 199 LAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEDLKQ--PTTLVQKFLGELWGCELDHSPLN 261
                                                   *************************************999..88********************* PP

                                     TIGR01015 261 vvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifpPrwlvaektf 325
                                                   vvawhGn vPykydl++fn+i++vsfdhpdPsiftvlt+p++ +G+a+ dfvifpPrw+vae+tf
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15550 262 VVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHGLANLDFVIFPPRWMVAENTF 326
                                                   ***************************************************************** PP

                                     TIGR01015 326 rPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasnaelkPekiddg 390
                                                   rPP++hrn+m efmGli+G+ydak+eGf pgGaslh++msahGPd e+  ka nael+P+kid+ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15550 327 RPPWFHRNLMNEFMGLIQGTYDAKAEGFLPGGASLHSCMSAHGPDGETCTKAINAELAPSKIDN- 390
                                                   ****************************************************************. PP

                                     TIGR01015 391 tlafmfesslslavtklakelekldedyeevwqglkk 427
                                                   t+afmfe+s +l+ +++a  + +l+++y+++w +l  
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_15550 391 TMAFMFETSQVLRPSRFALDCPQLQNNYDACWASLPV 427
                                                   *********************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (434 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: 00:00:00.02
# Mc/sec: 8.51
//
[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