GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoA in Shewanella loihica PV-4

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate 5210371 Shew_2814 thymidine phosphorylase (RefSeq)

Query= BRENDA::P07650
         (440 letters)



>FitnessBrowser__PV4:5210371
          Length = 443

 Score =  611 bits (1576), Expect = e-179
 Identities = 298/440 (67%), Positives = 358/440 (81%)

Query: 1   MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLT 60
           MFLAQEIIRKKR+G  LS +EI+FF+ GI +NT+SEGQIAAL M ++F DM M ER++LT
Sbjct: 1   MFLAQEIIRKKRNGEVLSTQEIQFFVQGITNNTVSEGQIAALGMAVYFKDMNMDERIALT 60

Query: 61  MAMRDSGTVLDWKSLHLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYIPMISGRGLGHT 120
            AMRDSGTVL+WK+L L+GPI+DKHSTGGVGDV SLMLGPM AACGGY+PMISGRGLGHT
Sbjct: 61  TAMRDSGTVLNWKNLGLDGPIIDKHSTGGVGDVISLMLGPMAAACGGYVPMISGRGLGHT 120

Query: 121 GGTLDKLESIPGFDIFPDDNRFREIIKDVGVAIIGQTSSLAPADKRFYATRDITATVDSI 180
           GGTLDK ++IPG+   PD + FR+++K+ GVAIIGQT  L PADKRFY+ RD TATV+SI
Sbjct: 121 GGTLDKFDAIPGYQTEPDSDLFRKVVKEAGVAIIGQTGDLVPADKRFYSIRDNTATVESI 180

Query: 181 PLITASILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLT 240
            LITASIL+KKLA GLDAL MDVKVGSGAFMPTYE SE LA +I  VANGAG +TTALLT
Sbjct: 181 SLITASILSKKLAAGLDALAMDVKVGSGAFMPTYEASEELARSITAVANGAGTKTTALLT 240

Query: 241 DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGKLAKDDAEARAKL 300
           DMNQVLAS AGNAVEV+EAV FLTG YRNPRL++VTM LC EML  G LA  +A+AR KL
Sbjct: 241 DMNQVLASCAGNAVEVKEAVDFLTGAYRNPRLYEVTMGLCAEMLQLGGLAASEADAREKL 300

Query: 301 QAVLDNGKAAEVFGRMVAAQKGPTDFVENYAKYLPTAMLTKAVYADTEGFVSEMDTRALG 360
             VLDNGKAA++FGRM+A   GP DF+ENYAKYLP + + + VYAD  GF + MDTR LG
Sbjct: 301 NRVLDNGKAADIFGRMIAGLGGPADFIENYAKYLPQSQIIRPVYADRSGFAASMDTRELG 360

Query: 361 MAVVAMGGGRRQASDTIDYSVGFTDMARLGDQVDGQRPLAVIHAKDENNWQEAAKAVKAA 420
           +AVV +GGGRR+  D +DYSVG T +  LGD++   +P+A++HA+ E+ ++EAA AVK A
Sbjct: 361 LAVVTLGGGRRKPGDALDYSVGLTQVCALGDEITSDKPIAMVHAQSESAFEEAAAAVKKA 420

Query: 421 IKLADKAPESTPTVYRRISE 440
           I + D+APE TP +YR I +
Sbjct: 421 IHIGDEAPEKTPEIYRYIRQ 440


Lambda     K      H
   0.318    0.134    0.377 

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: 553
Number of extensions: 11
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: 440
Length of database: 443
Length adjustment: 32
Effective length of query: 408
Effective length of database: 411
Effective search space:   167688
Effective search space used:   167688
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 5210371 Shew_2814 (thymidine phosphorylase (RefSeq))
to HMM TIGR02643 (deoA: 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/TIGR02643.hmm
# target sequence database:        /tmp/gapView.12154.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02643  [M=437]
Accession:   TIGR02643
Description: T_phosphoryl: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   4.5e-226  736.7   4.9   5.1e-226  736.5   4.9    1.0  1  lcl|FitnessBrowser__PV4:5210371  Shew_2814 thymidine phosphorylas


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210371  Shew_2814 thymidine phosphorylase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  736.5   4.9  5.1e-226  5.1e-226       1     437 []       2     438 ..       2     438 .. 1.00

  Alignments for each domain:
  == domain 1  score: 736.5 bits;  conditional E-value: 5.1e-226
                        TIGR02643   1 llpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvldwkdldlng 78 
                                      +l+qeiirkkr+g+ ls++ei+ fv+g+t+++vsegqiaal mavyf+++++de++alt amrdsG+vl+wk+l l+g
  lcl|FitnessBrowser__PV4:5210371   2 FLAQEIIRKKRNGEVLSTQEIQFFVQGITNNTVSEGQIAALGMAVYFKDMNMDERIALTTAMRDSGTVLNWKNLGLDG 79 
                                      79**************************************************************************** PP

                        TIGR02643  79 PvvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPdeelfrkvvkdvGvaiiGqt 156
                                      P++dkhstGGvGdv+slml+P+ aacGgyvPmisGrGlGhtGGtldk++aiPGy++ Pd++lfrkvvk++GvaiiGqt
  lcl|FitnessBrowser__PV4:5210371  80 PIIDKHSTGGVGDVISLMLGPMAAACGGYVPMISGRGLGHTGGTLDKFDAIPGYQTEPDSDLFRKVVKEAGVAIIGQT 157
                                      ****************************************************************************** PP

                        TIGR02643 157 adlaPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnGafmesleeseelarslvevangaGvrt 234
                                      +dl Padkr+y+ird tatvesi+litasilskklaaGldal++dvkvG+Gafm+++e seelars+  vangaG +t
  lcl|FitnessBrowser__PV4:5210371 158 GDLVPADKRFYSIRDNTATVESISLITASILSKKLAAGLDALAMDVKVGSGAFMPTYEASEELARSITAVANGAGTKT 235
                                      ****************************************************************************** PP

                        TIGR02643 235 talitdmnqalasaaGnavevreavdfltGekrdkrleevtlalaaellvsgklaadeaeaeakleavlesGraaerf 312
                                      tal+tdmnq+las+aGnavev+eavdfltG++r++rl evt+ l+ae+l+ g+laa+ea+a+ kl++vl++G+aa++f
  lcl|FitnessBrowser__PV4:5210371 236 TALLTDMNQVLASCAGNAVEVKEAVDFLTGAYRNPRLYEVTMGLCAEMLQLGGLAASEADAREKLNRVLDNGKAADIF 313
                                      ****************************************************************************** PP

                        TIGR02643 313 armvaalgGPadfvekpekylakaaiakavkaaregylseidtrelGlavvalGGGrrkaddkldlsvGltdllelGe 390
                                      +rm+a lgGPadf+e+++kyl++++i+++v+a+r+g+ +++dtrelGlavv+lGGGrrk+ d ld+svGlt++  lG+
  lcl|FitnessBrowser__PV4:5210371 314 GRMIAGLGGPADFIENYAKYLPQSQIIRPVYADRSGFAASMDTRELGLAVVTLGGGRRKPGDALDYSVGLTQVCALGD 391
                                      ****************************************************************************** PP

                        TIGR02643 391 kvekeeplavvhaadeedaeeaakavkkalkiadeaPeeakvvleri 437
                                      ++ +++p+a+vha++e+ +eeaa+avkka++i+deaPe+++ +++ i
  lcl|FitnessBrowser__PV4:5210371 392 EITSDKPIAMVHAQSESAFEEAAAAVKKAIHIGDEAPEKTPEIYRYI 438
                                      *******************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (437 nodes)
Target sequences:                          1  (443 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 0.01s 00:00:00.02 Elapsed: 00:00:00.03
# Mc/sec: 4.97
//
[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