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

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.3530.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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 11.96
//
[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