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_3100 Echvi_3100 mannonate dehydratase

Query= BRENDA::P24215
         (394 letters)



>FitnessBrowser__Cola:Echvi_3100
          Length = 382

 Score =  467 bits (1201), Expect = e-136
 Identities = 227/382 (59%), Positives = 291/382 (76%), Gaps = 6/382 (1%)

Query: 6   RWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSVVESV 65
           RWYGP DPV+LAD+RQAGATG+V+ALHH+PNG +WS EEI KRK  IE AGL WSVVES+
Sbjct: 2   RWYGPQDPVTLADIRQAGATGIVSALHHLPNGVIWSREEIKKRKDTIEAAGLTWSVVESI 61

Query: 66  PIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDGSKA 125
           P+HE+IKT +GNY+++IANY+ ++ NLA  GI TVCYNFMPVLDWTRTDL Y LP+G+KA
Sbjct: 62  PVHENIKTRSGNYQEYIANYKTSIGNLAAEGIHTVCYNFMPVLDWTRTDLAYELPNGAKA 121

Query: 126 LRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGLPGAE 185
           LRF+    AAF++ IL+RP AE DY+E+ I +A   F  M+++ +  LT NIIAGLPGAE
Sbjct: 122 LRFELQALAAFDLFILQRPNAEKDYSEQVIKRAEAYFKEMTEDAEQLLTNNIIAGLPGAE 181

Query: 186 EGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPILGLP 245
           EGY+L  F++ L+ Y+ ID  KL  N  +FL+ IIP AE+  V MA+HPDDPP P+ GLP
Sbjct: 182 EGYSLKAFQQVLDTYQHIDADKLATNLRLFLEEIIPTAEKNRVFMAIHPDDPPFPMFGLP 241

Query: 246 RIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRSTMRE 305
           R++STI+D++ +V    S  NG T CTGS+GVRADNDL  +I++ G  I+F HLRST R 
Sbjct: 242 RVMSTIDDVKRLVTETPSEYNGITFCTGSFGVRADNDLPQIIREHGDHIHFIHLRSTQR- 300

Query: 306 DNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKKKTN 365
           D    FHEA HL GDV +  V+K +++ + RR+       +PMRPDHGHQMLDDL+K TN
Sbjct: 301 DAYGNFHEANHLEGDVPIVAVIKELIKVQSRRQKS-----LPMRPDHGHQMLDDLRKTTN 355

Query: 366 PGYSAIGRLKGLAEVRGVELAI 387
           PGY+ IGRLKGLAE+RG+E+ +
Sbjct: 356 PGYTGIGRLKGLAELRGLEMGL 377


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: 510
Number of extensions: 17
Number of successful extensions: 3
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: 382
Length adjustment: 30
Effective length of query: 364
Effective length of database: 352
Effective search space:   128128
Effective search space used:   128128
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_3100 Echvi_3100 (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.318.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   5.6e-171  554.9   0.0   6.7e-171  554.6   0.0    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3100  Echvi_3100 mannonate dehydratase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3100  Echvi_3100 mannonate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  554.6   0.0  6.7e-171  6.7e-171       6     387 ..       2     377 ..       1     380 [. 0.98

  Alignments for each domain:
  == domain 1  score: 554.6 bits;  conditional E-value: 6.7e-171
                            TIGR00695   6 rwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeiklqteeye 79 
                                          rwyG++dpv+l+d+rqaGa+Giv alhh pnG +w+ eeikkrk++ie aGl++svves+pvhe+ik+++++y+
  lcl|FitnessBrowser__Cola:Echvi_3100   2 RWYGPQDPVTLADIRQAGATGIVSALHHLPNGVIWSREEIKKRKDTIEAAGLTWSVVESIPVHENIKTRSGNYQ 75 
                                          9************************************************************************* PP

                            TIGR00695  80 kyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpdaekdytee 153
                                          +yi+nyk ++ nla  Gi++vcynfmpvldwtrtdlayel++G+kalrf+  ++aa++l+il+rp+aekdy+e+
  lcl|FitnessBrowser__Cola:Echvi_3100  76 EYIANYKTSIGNLAAEGIHTVCYNFMPVLDWTRTDLAYELPNGAKALRFELQALAAFDLFILQRPNAEKDYSEQ 149
                                          ************************************************************************** PP

                            TIGR00695 154 elvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevG 227
                                           + ra  ++++m+e+    lt niiaglpGaeeg+ l+ +++ l++y+ id +kl +nl +fl+ei+p ae+  
  lcl|FitnessBrowser__Cola:Echvi_3100 150 VIKRAEAYFKEMTEDAEQLLTNNIIAGLPGAEEGYSLKAFQQVLDTYQHIDADKLATNLRLFLEEIIPTAEKNR 223
                                          *************9999999****************************************************** PP

                            TIGR00695 228 vkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadriyfahlrs 301
                                          v maihpddpp p++Glpr++sti+d+k+lv  ++s  ngit+ctGs+Gvradndl +++++++d i+f hlrs
  lcl|FitnessBrowser__Cola:Echvi_3100 224 VFMAIHPDDPPFPMFGLPRVMSTIDDVKRLVTETPSEYNGITFCTGSFGVRADNDLPQIIREHGDHIHFIHLRS 297
                                          ************************************************************************** PP

                            TIGR00695 302 vkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlk 375
                                          ++r+  + +fhea hle+dv +  v+k +++ + rr++      +p+rpdhG+q+lddl+k tnpGy+ igrlk
  lcl|FitnessBrowser__Cola:Echvi_3100 298 TQRDAYG-NFHEANHLEGDVPIVAVIKELIKVQSRRQKS-----LPMRPDHGHQMLDDLRKTTNPGYTGIGRLK 365
                                          ******9.***************9999999988888765.....5***************************** PP

                            TIGR00695 376 GlaelrGlelal 387
                                          GlaelrGle+ l
  lcl|FitnessBrowser__Cola:Echvi_3100 366 GLAELRGLEMGL 377
                                          *********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (394 nodes)
Target sequences:                          1  (382 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: 9.10
//
[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