GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Echinicola vietnamensis KMM 6221, DSM 17526

Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate Echvi_1869 Echvi_1869 mannonate dehydratase

Query= BRENDA::P24215
         (394 letters)



>FitnessBrowser__Cola:Echvi_1869
          Length = 387

 Score =  425 bits (1093), Expect = e-123
 Identities = 212/388 (54%), Positives = 276/388 (71%), Gaps = 7/388 (1%)

Query: 3   QTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSVV 62
           QTWRWYGPNDPVSL DVRQAGATGVV+ALH IP+G+ W ++ I +RKA IE AGL WSVV
Sbjct: 5   QTWRWYGPNDPVSLQDVRQAGATGVVSALHQIPHGDEWPIQLIQERKATIEAAGLEWSVV 64

Query: 63  ESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDG 122
           ESVP+HE IKT   + E ++ NY++TLRNL++CGI+TVCYNFMPVLDWTRTDL   L +G
Sbjct: 65  ESVPVHEAIKTRNDHAEYYLENYRKTLRNLSKCGIKTVCYNFMPVLDWTRTDLALPLANG 124

Query: 123 SKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGLP 182
           +KAL  D  + A F++ IL R G EA Y  E +A+  ER+A M+ E +A L   ++ G+P
Sbjct: 125 AKALYLDWTDLAVFDLKILGRAGGEAFYKPEILAKVEERYAAMTKEQQAALQEIVLMGVP 184

Query: 183 GAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPIL 242
             E G TL+  ++ +E+Y  I K  L+EN   FL+ I  V EE G+RM +HPDDPP PIL
Sbjct: 185 -TEGGVTLEALQESIEVYSSIGKHGLQENLTYFLENIAEVCEEEGIRMTIHPDDPPFPIL 243

Query: 243 GLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRST 302
           GLPRI S+ ED+++++  V+   NG   CTGS G    NDL  M+   G R+YF HLR+ 
Sbjct: 244 GLPRIASSKEDLEFILQAVDRPFNGICFCTGSLGAGDHNDLPAMLDAVGDRVYFAHLRN- 302

Query: 303 MREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKK 362
           +++D    FHE+ HL+GDVDM  +++ +V+   +R        IP RPDHGHQMLDDL+K
Sbjct: 303 VKKDALGNFHESDHLDGDVDMCAIMERLVKLNAQR-----HQAIPFRPDHGHQMLDDLQK 357

Query: 363 KTNPGYSAIGRLKGLAEVRGVELAIQRA 390
            TNPGYSAIGRLKGLAE+RG+E+ I+ +
Sbjct: 358 VTNPGYSAIGRLKGLAELRGLEMGIKNS 385


Lambda     K      H
   0.320    0.136    0.410 

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: 453
Number of extensions: 23
Number of successful extensions: 4
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: 394
Length of database: 387
Length adjustment: 31
Effective length of query: 363
Effective length of database: 356
Effective search space:   129228
Effective search space used:   129228
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 Echvi_1869 Echvi_1869 (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.5990.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   7.3e-153  495.3   0.0   8.6e-153  495.0   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1869  Echvi_1869 mannonate dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1869  Echvi_1869 mannonate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.0   0.0  8.6e-153  8.6e-153       3     389 ..       5     384 ..       1     386 [. 0.98

  Alignments for each domain:
  == domain 1  score: 495.0 bits;  conditional E-value: 8.6e-153
                            TIGR00695   3 qtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeiklqte 76 
                                          qt+rwyG+ndpvsl+dvrqaGa+G+v alh+ip G+ w ++ i++rk++ie aGl++svvesvpvhe+ik++++
  lcl|FitnessBrowser__Cola:Echvi_1869   5 QTWRWYGPNDPVSLQDVRQAGATGVVSALHQIPHGDEWPIQLIQERKATIEAAGLEWSVVESVPVHEAIKTRND 78 
                                          8************************************************************************* PP

                            TIGR00695  77 eyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpdaekdy 150
                                          + e y+eny++tlrnl++cGik+vcynfmpvldwtrtdla +l +G+kal++d  ++a ++l+il r + e+ y
  lcl|FitnessBrowser__Cola:Echvi_1869  79 HAEYYLENYRKTLRNLSKCGIKTVCYNFMPVLDWTRTDLALPLANGAKALYLDWTDLAVFDLKILGRAGGEAFY 152
                                          ************************************************************************** PP

                            TIGR00695 151 teeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkeilpvae 224
                                          + e l++  e+++ m++e++a l   ++ g+p  e g +l+ ++e +e y +i ++ l+enl++fl++i  v e
  lcl|FitnessBrowser__Cola:Echvi_1869 153 KPEILAKVEERYAAMTKEQQAALQEIVLMGVPT-EGGVTLEALQESIEVYSSIGKHGLQENLTYFLENIAEVCE 225
                                          ********************************5.899************************************* PP

                            TIGR00695 225 evGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadriyfah 298
                                          e G++m+ihpddpp pilGlpri s++ed++ + + +d p ngi +ctGs+G+   ndl  + +  +dr+yfah
  lcl|FitnessBrowser__Cola:Echvi_1869 226 EEGIRMTIHPDDPPFPILGLPRIASSKEDLEFILQAVDRPFNGICFCTGSLGAGDHNDLPAMLDAVGDRVYFAH 299
                                          ************************************************************************** PP

                            TIGR00695 299 lrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaig 372
                                          lr+vk++  + +fhe+ hl++dvd+     a++e + + +a+  ++ ip rpdhG+q+lddl+k tnpGysaig
  lcl|FitnessBrowser__Cola:Echvi_1869 300 LRNVKKDALG-NFHESDHLDGDVDMC----AIMERLVKLNAQR-HQAIPFRPDHGHQMLDDLQKVTNPGYSAIG 367
                                          ******9999.***************....9999998888886.7889************************** PP

                            TIGR00695 373 rlkGlaelrGlelalkk 389
                                          rlkGlaelrGle+ +k+
  lcl|FitnessBrowser__Cola:Echvi_1869 368 RLKGLAELRGLEMGIKN 384
                                          *************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (387 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.82
//
[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