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

GapMind for catabolism of small carbon sources

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

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate AO356_28530 AO356_28530 mannonate dehydratase

Query= BRENDA::Q1QT83
         (391 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28530
          Length = 391

 Score =  588 bits (1515), Expect = e-172
 Identities = 278/388 (71%), Positives = 331/388 (85%)

Query: 1   MEHTWRWFGPDDPITLDEIRQTGATGIVTALHEIPNGEIWPEAAIAERKRLIEASGLAWS 60
           ME TWRWFGP DPI+L +IRQTGATGIVTALHEIPNGE+WP  AIA RK+LIEA+GL+WS
Sbjct: 1   MEQTWRWFGPKDPISLADIRQTGATGIVTALHEIPNGEVWPVDAIAARKQLIEAAGLSWS 60

Query: 61  VVESVPVHEDIKQGRGDCETHIARYQQTLRNLAACGIDVVCYNFMPVLDWTRTDLAWPLP 120
           VVES+PVHEDIK+G G  + +IA YQQ++RNLA+CGID+VCYNFMPVLDWTRTDL++ L 
Sbjct: 61  VVESIPVHEDIKRGCGRRDEYIANYQQSVRNLASCGIDIVCYNFMPVLDWTRTDLSFELA 120

Query: 121 GGGTALRFDQTAFAAFDLYLLERPGAEADYDATERDAARAYLDGLDESARQRLIDTIIAG 180
            GG ALRFDQTAFAAFDL++L+RPGA+A+Y A +   A+AY + L  + R+ L++T+IAG
Sbjct: 121 DGGWALRFDQTAFAAFDLFILQRPGAQAEYSAEDIQQAKAYFEQLTPARRETLVNTLIAG 180

Query: 181 LPGAEEHYSLARFREVIAEYAEIDAERLRDNLGHFLRAVVPVAEEVGIRLAIHPDDPPRP 240
           LPGAEEHYSL  FR+++  YA+ID  +LR++LG+FLRAV+PVAE VG+R+AIHPDDPPR 
Sbjct: 181 LPGAEEHYSLDNFRDLLRTYADIDEAKLREHLGYFLRAVIPVAEAVGVRMAIHPDDPPRA 240

Query: 241 LLGLPRVVSTPRDVQWILDAAPSPANGLTFCTGSYGVSAAIDLVAMGERFAERIYFAHLR 300
           LLGLPR++ST  D QW+LDAAPSPANGLTFCTGSYGV    DLVAM + FA  IYF HLR
Sbjct: 241 LLGLPRILSTAEDAQWLLDAAPSPANGLTFCTGSYGVREDNDLVAMAKHFAPFIYFTHLR 300

Query: 301 ATQRENDPRSFHESAHLDGDVDMVGVIKALVGEERRRERDGGPRLPLRPDHGHHLLDDLS 360
           +T+RE DPRSFHE+ HLDGDVDMVGVI ALV EERRRER+GGPRLPLRPDHGH LLDD  
Sbjct: 301 STRRETDPRSFHEAHHLDGDVDMVGVIGALVAEERRREREGGPRLPLRPDHGHQLLDDQH 360

Query: 361 RDTRPGYPLIGRLKGLAELRGVETAIKQ 388
           R + PGY LIGRLKGLAE+RGVE A+++
Sbjct: 361 RKSNPGYSLIGRLKGLAEIRGVELAVRR 388


Lambda     K      H
   0.321    0.139    0.430 

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: 523
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: 391
Length of database: 391
Length adjustment: 31
Effective length of query: 360
Effective length of database: 360
Effective search space:   129600
Effective search space used:   129600
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: 50 (23.9 bits)

Align candidate AO356_28530 AO356_28530 (mannonate dehydratase)
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

# 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/TIGR00695.hmm
# target sequence database:        /tmp/gapView.11710.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00695  [M=394]
Accession:   TIGR00695
Description: uxuA: mannonate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   3.3e-185  601.8   0.0     4e-185  601.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28530  AO356_28530 mannonate dehydratas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28530  AO356_28530 mannonate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  601.5   0.0    4e-185    4e-185       1     389 [.       1     388 [.       1     390 [. 0.99

  Alignments for each domain:
  == domain 1  score: 601.5 bits;  conditional E-value: 4e-185
                                       TIGR00695   1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvve 63 
                                                     meqt+rw+G++dp+sl+d+rq Ga+Givtalh+ipnGevw v+ i +rk+ ie aGls+svve
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28530   1 MEQTWRWFGPKDPISLADIRQTGATGIVTALHEIPNGEVWPVDAIAARKQLIEAAGLSWSVVE 63 
                                                     9************************************************************** PP

                                       TIGR00695  64 svpvheeiklqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskal 126
                                                     s+pvhe+ik + + +++yi+ny+q++rnla cGi++vcynfmpvldwtrtdl +el dG  al
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28530  64 SIPVHEDIKRGCGRRDEYIANYQQSVRNLASCGIDIVCYNFMPVLDWTRTDLSFELADGGWAL 126
                                                     *************************************************************** PP

                                       TIGR00695 127 rfdkikvaalelhilkrpdaekdyteeelvraveeasdmseedkarltrniiaglpGaeegek 189
                                                     rfd+ ++aa++l+il+rp+a+++y+ e++ +a+ ++++++   +  l+  +iaglpGaee + 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28530 127 RFDQTAFAAFDLFILQRPGAQAEYSAEDIQQAKAYFEQLTPARRETLVNTLIAGLPGAEEHYS 189
                                                     *************************************************************** PP

                                       TIGR00695 190 ldrikelleaykdideeklrenlafflkeilpvaeevGvkmaihpddpprpilGlprivstie 252
                                                     ld++++ll +y dide+klre+l +fl++++pvae+vGv+maihpddppr +lGlpri+st e
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28530 190 LDNFRDLLRTYADIDEAKLREHLGYFLRAVIPVAEAVGVRMAIHPDDPPRALLGLPRILSTAE 252
                                                     *************************************************************** PP

                                       TIGR00695 253 dmkklveisdspangitlctGsyGvradndlvelakqfadriyfahlrsvkreenpktfheaa 315
                                                     d ++l + ++spang+t+ctGsyGvr dndlv +ak+fa+ iyf+hlrs++re +p++fhea 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28530 253 DAQWLLDAAPSPANGLTFCTGSYGVREDNDLVAMAKHFAPFIYFTHLRSTRRETDPRSFHEAH 315
                                                     *************************************************************** PP

                                       TIGR00695 316 hlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlkGla 378
                                                     hl++dvd+  v+ a++ ee rr+ eG  +l p+rpdhG+qlldd ++k+npGys+igrlkGla
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28530 316 HLDGDVDMVGVIGALVAEERRREREGGPRL-PLRPDHGHQLLDDQHRKSNPGYSLIGRLKGLA 377
                                                     **************************6665.8******************************* PP

                                       TIGR00695 379 elrGlelalkk 389
                                                     e+rG+ela+++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_28530 378 EIRGVELAVRR 388
                                                     ********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (391 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: 8.08
//
[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