Aligments for a candidate for hmgA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for hmgA in Pseudomonas simiae WCS417

Align Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (characterized)
to candidate GFF989 PS417_05015 homogentisate 1,2-dioxygenase

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



>lcl|FitnessBrowser__WCS417:GFF989 PS417_05015 homogentisate
           1,2-dioxygenase
          Length = 427

 Score =  816 bits (2108), Expect = 0.0
 Identities = 386/425 (90%), Positives = 405/425 (95%)

Query: 10  LVYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYTELFSGTAFTMARSEARRTWMYRIQ 69
           L Y SGFGNEF+SEALPGALP+GQNSPQKAPYGLYTELFSGTAFTM RSEARRTW+YRIQ
Sbjct: 3   LEYLSGFGNEFASEALPGALPIGQNSPQKAPYGLYTELFSGTAFTMVRSEARRTWLYRIQ 62

Query: 70  PSANHPAFVKLERQLAGGPLGDVTPNRLRWNPLEIPGEPTDFIDGLVRMAANSGSEKPAG 129
           PSANHPAF+KLERQLAGGPLG VTPNRLRWNPL++P EPTDFIDGLV M ANSG+EKP+G
Sbjct: 63  PSANHPAFIKLERQLAGGPLGAVTPNRLRWNPLDMPSEPTDFIDGLVGMVANSGAEKPSG 122

Query: 130 ISIYHYRANRSMERVFFNADGEWLLVPEQGRLRIATELGVLELEPLEIAVLPRGLKFRIE 189
           ISIY YRANRSMERVFFNADGE L+VPE GRLRIATELGVLE+EPLEI VLPRGLKFR+E
Sbjct: 123 ISIYTYRANRSMERVFFNADGELLIVPELGRLRIATELGVLEVEPLEIVVLPRGLKFRVE 182

Query: 190 LLDPQARGYLAENHGAPLRLPDLGPIGSNGLANPRDFLTPVAHYEDLKQPTTLVQKFLGE 249
           LLD QARGY+AENHGAPLRLPDLGPIGSNGLANPRDFLTPVA YED+K+PTTLVQKFLGE
Sbjct: 183 LLDTQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVARYEDVKKPTTLVQKFLGE 242

Query: 250 LWGCELDHSPLNVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVHGLAN 309
           LW CELDHSPLNVVAWHGNNVPYKYDLRRFNT+GTVSFDHPDPSIFTVLTSPTS HGLAN
Sbjct: 243 LWACELDHSPLNVVAWHGNNVPYKYDLRRFNTLGTVSFDHPDPSIFTVLTSPTSTHGLAN 302

Query: 310 LDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGTYDAKAEGFLPGGASLHSCMSAHG 369
           LDFVIFPPRWMVAENTFRPPWFHRNLMNE+MGLIQG YDAKAEGFLPGGASLHSCMSAHG
Sbjct: 303 LDFVIFPPRWMVAENTFRPPWFHRNLMNEYMGLIQGAYDAKAEGFLPGGASLHSCMSAHG 362

Query: 370 PDGETCTKAINAELAPSKIDNTMAFMFETSQVLRPSRFALDCPQLQNNYDACWASLPVTF 429
           PDGETCTKAIN +LAP KIDNTMAFMFETSQVLRP++FALDCPQLQN YDACWASLP TF
Sbjct: 363 PDGETCTKAINVDLAPHKIDNTMAFMFETSQVLRPTQFALDCPQLQNTYDACWASLPATF 422

Query: 430 NPNRR 434
           NPNRR
Sbjct: 423 NPNRR 427


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: 857
Number of extensions: 21
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: 427
Length adjustment: 32
Effective length of query: 402
Effective length of database: 395
Effective search space:   158790
Effective search space used:   158790
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 GFF989 PS417_05015 (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.18024.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   7.9e-196  636.8   0.0     9e-196  636.6   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF989  PS417_05015 homogentisate 1,2-di


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF989  PS417_05015 homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  636.6   0.0    9e-196    9e-196       2     428 ..       3     421 ..       2     422 .. 0.97

  Alignments for each domain:
  == domain 1  score: 636.6 bits;  conditional E-value: 9e-196
                          TIGR01015   2 lkylsGfgnefeseavpgalPvGqnsPqkapyglyaeqlsGsaftaPraenkrswlyrirPsaaheafeelkesee 77 
                                        l+ylsGfgnef+sea+pgalP GqnsPqkapygly+e +sG+aft+ r+e +r+wlyri+Psa+h af +l+   +
  lcl|FitnessBrowser__WCS417:GFF989   3 LEYLSGFGNEFASEALPGALPIGQNSPQKAPYGLYTELFSGTAFTMVRSEARRTWLYRIQPSANHPAFIKLE--RQ 76 
                                        79*****************************************************************99998..44 PP

                          TIGR01015  78 kltanfkeeasdpnqlrwspleipseeavdfveglvtlagagdaksraGlavhlyavnasmedevfynadGdlliv 153
                                            +    a++pn+lrw+pl++ps e +df++glv + +++ a++ +G+++++y +n sm ++vf+nadG+lliv
  lcl|FitnessBrowser__WCS417:GFF989  77 LAGGPL--GAVTPNRLRWNPLDMPS-EPTDFIDGLVGMVANSGAEKPSGISIYTYRANRSM-ERVFFNADGELLIV 148
                                        555554..47789***********8.99*********************************.89************ PP

                          TIGR01015 154 pqkGaleittelGrlkvePneiaviprGvrfrveve.eearGyilevygakfqlPdlGPiGanglanprdfeaPva 228
                                        p+ G l+i telG+l+veP ei+v+prG++frve+   +arGy+ e++ga  +lPdlGPiG+nglanprdf +Pva
  lcl|FitnessBrowser__WCS417:GFF989 149 PELGRLRIATELGVLEVEPLEIVVLPRGLKFRVELLdTQARGYVAENHGAPLRLPDLGPIGSNGLANPRDFLTPVA 224
                                        **********************************99788************************************* PP

                          TIGR01015 229 afedkevkdevrviskfqgklfaakqdhspldvvawhGnyvPykydlkkfnvinsvsfdhpdPsiftvltapsdke 304
                                         +ed +   ++++++kf g+l+a++ dhspl+vvawhGn vPykydl++fn++++vsfdhpdPsiftvlt+p++++
  lcl|FitnessBrowser__WCS417:GFF989 225 RYEDVKK--PTTLVQKFLGELWACELDHSPLNVVAWHGNNVPYKYDLRRFNTLGTVSFDHPDPSIFTVLTSPTSTH 298
                                        ***9888..89***************************************************************** PP

                          TIGR01015 305 GtaiadfvifpPrwlvaektfrPPyyhrnvmsefmGlikGkydakeeGfvpgGaslhnimsahGPdveafekasna 380
                                        G+a+ dfvifpPrw+vae+tfrPP++hrn+m e+mGli+G+ydak+eGf pgGaslh++msahGPd e+  ka n+
  lcl|FitnessBrowser__WCS417:GFF989 299 GLANLDFVIFPPRWMVAENTFRPPWFHRNLMNEYMGLIQGAYDAKAEGFLPGGASLHSCMSAHGPDGETCTKAINV 374
                                        **************************************************************************** PP

                          TIGR01015 381 elkPekiddgtlafmfesslslavtklakelekldedyeevwqglkkk 428
                                        +l+P+kid+ t+afmfe+s +l+ t++a  + +l++ y+++w +l   
  lcl|FitnessBrowser__WCS417:GFF989 375 DLAPHKIDN-TMAFMFETSQVLRPTQFALDCPQLQNTYDACWASLPAT 421
                                        *********.*********************************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (429 nodes)
Target sequences:                          1  (427 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 7.62
//
[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, or view the source code.

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