Alignments for a candidate for hmgA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for hmgA in Pseudomonas fluorescens FW300-N2C3

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate AO356_16825 AO356_16825 homogentisate 1,2-dioxygenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_5290
         (434 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_16825
          Length = 434

 Score =  869 bits (2245), Expect = 0.0
 Identities = 415/434 (95%), Positives = 423/434 (97%)

Query: 1   MNLVSPASDLAYQSGFGNEFASEALPGALPVGQNSPQKVPYGLYAELFSGTAFTMARSEA 60
           MNL S  SDLAYQSG GNEFASEALPGALP+GQNSPQK PYGLYAELFSGTAFTMARSEA
Sbjct: 1   MNLDSTMSDLAYQSGLGNEFASEALPGALPIGQNSPQKAPYGLYAELFSGTAFTMARSEA 60

Query: 61  RRTWMYRIRPSANHPAFTRLERQLAGGPLGEVTPNRLRWNPLEIPAEPTDFIDGLVCMAA 120
           RRTWMYRIRPSANHPAFTRLERQLAGGPLGEVTPNRLRWNPL+IPAEPTDF+DGLVCMAA
Sbjct: 61  RRTWMYRIRPSANHPAFTRLERQLAGGPLGEVTPNRLRWNPLDIPAEPTDFLDGLVCMAA 120

Query: 121 NAGADKPAGISLYQYQANRSMERVFFNADGEWLIVPQLGRLRITTELGVLELAPLEIVVL 180
           NAGADKPAG+SLY Y+ANRSMERVFFNADGEWLIVPQLGRLRI TELGVLELAPLEI VL
Sbjct: 121 NAGADKPAGVSLYHYRANRSMERVFFNADGEWLIVPQLGRLRIATELGVLELAPLEIAVL 180

Query: 181 PRGLKFRIELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYENLAQPT 240
           PRGLKFR+ELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVA YENLAQPT
Sbjct: 181 PRGLKFRVELLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVARYENLAQPT 240

Query: 241 SLVQKFLGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300
           +LVQKFLGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS
Sbjct: 241 TLVQKFLGELWGCELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTS 300

Query: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGAS 360
           PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGG S
Sbjct: 301 PTSVHGLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGTS 360

Query: 361 LHSCMSAHGPDGETCTKAINAELQPVKIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDA 420
           LHSCMSAHGPDGETCTKAINA+LQP KIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDA
Sbjct: 361 LHSCMSAHGPDGETCTKAINADLQPAKIDNTMAFMFETSQVLRPSRFALDCPQLQTDYDA 420

Query: 421 CWASLPVTFDPTRR 434
           CWASLPVTFDPTRR
Sbjct: 421 CWASLPVTFDPTRR 434


Lambda     K      H
   0.321    0.138    0.435 

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: 915
Number of extensions: 24
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 AO356_16825 AO356_16825 (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.28869.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.3e-193  628.7   0.0   2.6e-193  628.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16825  AO356_16825 homogentisate 1,2-di


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16825  AO356_16825 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  628.5   0.0  2.6e-193  2.6e-193       2     427 ..      10     427 ..       9     429 .. 0.97

  Alignments for each domain:
  == domain 1  score: 628.5 bits;  conditional E-value: 2.6e-193
                                       TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsa 64 
                                                     l+y+sG+gnef+sea+pgalP GqnsPqkapyglyae +sG+aft+ r+e +r+w+yrirPsa
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16825  10 LAYQSGLGNEFASEALPGALPIGQNSPQKAPYGLYAELFSGTAFTMARSEARRTWMYRIRPSA 72 
                                                     79************************************************************* PP

                                       TIGR01015  65 aheafeelkeseekltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGl 127
                                                     +h af++l+   +    +    +++pn+lrw+pl+ip+ e +df++glv +a+++ a + aG+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16825  73 NHPAFTRLE--RQLAGGPLG--EVTPNRLRWNPLDIPA-EPTDFLDGLVCMAANAGADKPAGV 130
                                                     ***999998..455555555..5679***********6.9*********************** PP

                                       TIGR01015 128 avhlyavnasmedevfynadGdllivpqkGaleittelGrlkvePneiaviprGvrfrvevee 190
                                                     +++ y +n sm ++vf+nadG+ livpq G l+i telG+l+++P eiav+prG++frve+ +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16825 131 SLYHYRANRSM-ERVFFNADGEWLIVPQLGRLRIATELGVLELAPLEIAVLPRGLKFRVELLD 192
                                                     ***********.89***********************************************96 PP

                                       TIGR01015 191 e.arGyilevygakfqlPdlGPiGanglanprdfeaPvaafedkevkdevrviskfqgklfaa 252
                                                     + arGy+ e++ga  +lPdlGPiG+nglanprdf +Pva +e+     ++++++kf g+l+ +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16825 193 PqARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVARYENLAQ--PTTLVQKFLGELWGC 253
                                                     559***************************************9988..88************* PP

                                       TIGR01015 253 kqdhspldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdkeGtaiadfvifp 315
                                                     + dhspldvvawhGn vPykydl++fn+i++vsfdhpdPsiftvlt+p++ +G+a+ dfvifp
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16825 254 ELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHGLANLDFVIFP 316
                                                     *************************************************************** PP

                                       TIGR01015 316 PrwlvaektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekas 378
                                                     Prw+vae+tfrPP++hrn+m efmGli+G+ydak+eGf pgG+slh++msahGPd e+  ka 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16825 317 PRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAEGFLPGGTSLHSCMSAHGPDGETCTKAI 379
                                                     *************************************************************** PP

                                       TIGR01015 379 naelkPekiddgtlafmfesslslavtklakelekldedyeevwqglkk 427
                                                     na+l+P kid+ t+afmfe+s +l+ +++a  + +l++dy+++w +l  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_16825 380 NADLQPAKIDN-TMAFMFETSQVLRPSRFALDCPQLQTDYDACWASLPV 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 8.84
//
[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