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.12837.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 10.25
//
[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:

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:

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:

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:

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