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

GapMind for catabolism of small carbon sources

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

Align Putative thymidine phosphorylase; EC 2.4.2.4; TdRPase (uncharacterized)
to candidate Echvi_3166 Echvi_3166 putative thymidine phosphorylase

Query= curated2:Q2SLV0
         (505 letters)



>FitnessBrowser__Cola:Echvi_3166
          Length = 500

 Score =  536 bits (1381), Expect = e-157
 Identities = 265/494 (53%), Positives = 357/494 (72%)

Query: 7   NYLFLKRIGINTHQEPVVYMRQDCHVCRSEGFNAHSRVRVTTNKRSIIATVHQVTDGWLS 66
           N L  K +GI T  E VVYMR+DCHVC SEGF A +R+R++    SI+A+++ +    L 
Sbjct: 6   NILKYKHLGIYTQNENVVYMREDCHVCISEGFEALTRIRISNANTSIVASLNVLNSDILL 65

Query: 67  HQEAGLSDAAWRLLEAEDGEVAYFSHTKAVDSMSHVRGKLYGASLTQESADEVVKDVAGG 126
             E GLSDAA + L     +  Y SH + ++S+SHVR K+Y   L  ++ + ++ D+  G
Sbjct: 66  PNEIGLSDAAAKKLNVSQNDTLYVSHLEPIESLSHVRAKIYNKKLDYKAYNNIITDIVEG 125

Query: 127 LYSDVQLAAFVTACAGSRLNQDEVAALTSAMVKVGQRIDWGTSPIMDKHCVGGLPGNRTT 186
            YS++ L+AF+TACAG R++ DE++ LT AM+  G++++W    ++DKHC+GGLPGNRTT
Sbjct: 126 DYSNIHLSAFITACAGDRMDIDEISDLTKAMIASGKQLNWNKDIVVDKHCIGGLPGNRTT 185

Query: 187 PIVVAIVTACGLRMPKTSSRAITSPAGTADTMETMAPVNLTLAQMKKVVEQEGGCIAWGG 246
           P+VVAIV A GL MPKTSSRAITSPAGTADTME +  V L+  ++K VVE+EGGC  WGG
Sbjct: 186 PLVVAIVAAYGLTMPKTSSRAITSPAGTADTMEVLTNVTLSSEEIKTVVEKEGGCFVWGG 245

Query: 247 SVSLSPADDVLIRIERALDLDSEGQLVASVISKKVAAGSTHVLIDIPIGMTAKVRSPEYA 306
           +  LSPADDVLI+IE+ALD+DSEGQL+ASV+SKK AAGSTHV+IDIP+G TAKVRS E A
Sbjct: 246 TAQLSPADDVLIKIEKALDIDSEGQLIASVLSKKAAAGSTHVVIDIPVGETAKVRSTEMA 305

Query: 307 ERLASHMRYTGVKLGIQVEAMFTDGAQPVGRGIGPALEARDILAVLRNQAEAPADLRVRA 366
           E+L +HM   G  +G+ V+ + TDG QPVGRGIGP LEA DIL VL+N+ +AP DL  RA
Sbjct: 306 EKLKNHMETVGTAVGLNVKVVVTDGTQPVGRGIGPTLEAIDILKVLKNEEDAPKDLTERA 365

Query: 367 LTLAGRLLEIGGVASHGAGVARARETLESGAALHKFMAICEAQGGFREPALAPHCYEATA 426
           L LA  LLE+ G    G G+  A + L+SG A  KF+AIC+AQG F +P LAP+  E  A
Sbjct: 366 LLLATELLELSGKVEKGKGLETAHKILKSGKAYEKFIAICKAQGQFSKPVLAPYKIEIKA 425

Query: 427 DRVGVVSFVNNRFVAKLAKLAGAPSNSSAGVDFHVKLGQKVRVGEPLFSIYAEAPGELAY 486
           ++ GV+  ++NR +AKLAKL+GAP + SAG+  +V L +K+ + + L++IYAE+ GEL Y
Sbjct: 426 EKSGVLQRIDNRKIAKLAKLSGAPQSKSAGILLNVHLNEKIEIDQLLYTIYAESKGELNY 485

Query: 487 ALDFLRDHPNEIRI 500
           AL++  +H + I I
Sbjct: 486 ALEYKNNHNDIITI 499


Lambda     K      H
   0.318    0.132    0.382 

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: 616
Number of extensions: 10
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: 505
Length of database: 500
Length adjustment: 34
Effective length of query: 471
Effective length of database: 466
Effective search space:   219486
Effective search space used:   219486
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Echvi_3166 Echvi_3166 (putative thymidine phosphorylase)
to HMM TIGR02645 (putative thymidine phosphorylase (EC 2.4.2.4))

# 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/TIGR02645.hmm
# target sequence database:        /tmp/gapView.16267.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02645  [M=493]
Accession:   TIGR02645
Description: ARCH_P_rylase: putative thymidine phosphorylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                            -----------
   1.1e-184  600.4   9.3   1.3e-184  600.1   9.3    1.0  1  lcl|FitnessBrowser__Cola:Echvi_3166  Echvi_3166 putative thymidine ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_3166  Echvi_3166 putative thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  600.1   9.3  1.3e-184  1.3e-184       1     489 [.       8     496 ..       8     499 .. 0.97

  Alignments for each domain:
  == domain 1  score: 600.1 bits;  conditional E-value: 1.3e-184
                            TIGR02645   1 lkvrvlnidtgqekvlinskd...lkeekltpqdrvevrlgkkslia..ivvssddlvesgevglseevveele 69 
                                          lk ++l+i t++e+v+++ +d   + +e++++  r+++   + s++a  +v +s d++  +e+gls  + ++l+
  lcl|FitnessBrowser__Cola:Echvi_3166   8 LKYKHLGIYTQNENVVYMREDchvCISEGFEALTRIRISNANTSIVAslNVLNS-DILLPNEIGLSDAAAKKLN 80 
                                          6899*****************7777799*******************6545555.689999************* PP

                            TIGR02645  70 ekegdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalaingldvdeiealti 143
                                          ++++d   v++ e+ esl+ +r+k+++kkl+ +  ++i++div+  +s++++saf+ta+a +++d dei +lt+
  lcl|FitnessBrowser__Cola:Echvi_3166  81 VSQNDTLYVSHLEPIESLSHVRAKIYNKKLDYKAYNNIITDIVEGDYSNIHLSAFITACAGDRMDIDEISDLTK 154
                                          ************************************************************************** PP

                            TIGR02645 144 amvetGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaaGtaDvvevltrvelsve 217
                                          am+ +G++l+w+++++vDkh+iGG+PGn+t++lvv+ivaa GL++Pktssraits+aGtaD++evlt+v+ls+e
  lcl|FitnessBrowser__Cola:Echvi_3166 155 AMIASGKQLNWNKDIVVDKHCIGGLPGNRTTPLVVAIVAAYGLTMPKTSSRAITSPAGTADTMEVLTNVTLSSE 228
                                          ************************************************************************** PP

                            TIGR02645 218 elkrivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskkiaiGstkvliDiPvGpgakvksv 291
                                          e+k +vek ggc+vWGG  +l+PaDDvlik+e++L++D+e ql+as+lskk a+Gst+v+iDiPvG++akv+s 
  lcl|FitnessBrowser__Cola:Echvi_3166 229 EIKTVVEKEGGCFVWGGTAQLSPADDVLIKIEKALDIDSEGQLIASVLSKKAAAGSTHVVIDIPVGETAKVRST 302
                                          ************************************************************************** PP

                            TIGR02645 292 keaerLakdlielgkrlgvtvevvityGsqPiGraiGPaLeakealavLesskeaPtsLvekslaLaaiLLemg 365
                                          + ae+L+++++++g  +g +v+vv+t+G+qP+Gr+iGP+Lea ++l+vL+++++aP++L e++l La+ LLe++
  lcl|FitnessBrowser__Cola:Echvi_3166 303 EMAEKLKNHMETVGTAVGLNVKVVVTDGTQPVGRGIGPTLEAIDILKVLKNEEDAPKDLTERALLLATELLELS 376
                                          ************************************************************************** PP

                            TIGR02645 366 gaaergaGkelarelLdsGkaleklkeiieaqGgdniksedievGklkadikaetdGyvteidnkaltriarea 439
                                          g++e+g+G e a+++L+sGka+ek+  i++aqG     s+++ +  +k +ikae++G+ ++idn++++++a+++
  lcl|FitnessBrowser__Cola:Echvi_3166 377 GKVEKGKGLETAHKILKSGKAYEKFIAICKAQGQF---SKPVLA-PYKIEIKAEKSGVLQRIDNRKIAKLAKLS 446
                                          *********************************99...666655.9**************************** PP

                            TIGR02645 440 GaPedkgaGvklhvkvgdkvkkGdplytiyaeseekldkaialaralepi 489
                                          GaP+ k aG+ l+v++++k++  + lytiyaes+ +l++a+++ + ++ i
  lcl|FitnessBrowser__Cola:Echvi_3166 447 GAPQSKSAGILLNVHLNEKIEIDQLLYTIYAESKGELNYALEYKNNHNDI 496
                                          ******************************************99999877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (500 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: 00:00:00.03
# Mc/sec: 7.13
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
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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