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

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.32396.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 6.66
//
[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