Alignments for a candidate for deoA in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Shewanella oneidensis MR-1

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate 200396 SO1218 thymidine phosphorylase (NCBI ptt file)

Query= BRENDA::Q7CP66
         (440 letters)



>FitnessBrowser__MR1:200396
          Length = 443

 Score =  600 bits (1546), Expect = e-176
 Identities = 297/438 (67%), Positives = 353/438 (80%)

Query: 1   MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLT 60
           MFLAQEIIRKKR+G  LS EEI+FF+ GI  N +SEGQIAAL M ++F+DM M ER++LT
Sbjct: 1   MFLAQEIIRKKRNGLVLSAEEIQFFVKGITTNAVSEGQIAALGMAVYFNDMNMDERIALT 60

Query: 61  MAMRDSGTVLDWKSLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHT 120
            AMRDSGTVL+W+SLNLNGP++DKHSTGGVGDV SLMLGPM AACGGYVPMISGRGLGHT
Sbjct: 61  TAMRDSGTVLNWQSLNLNGPVIDKHSTGGVGDVISLMLGPMAAACGGYVPMISGRGLGHT 120

Query: 121 GGTLDKLEAIPGFDIFPDDNRFREIIQDVGVAIIGQTSSLAPADKRFYATRDITATVDSI 180
           GGTLDK +AIPG+   P    FR++++DVGVAIIGQT  L PADKRFY+ RD TATV+SI
Sbjct: 121 GGTLDKFDAIPGYQTEPSSELFRKVVKDVGVAIIGQTGDLVPADKRFYSIRDNTATVESI 180

Query: 181 PLITGSILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLT 240
            LIT SIL+KKLA  LDAL MDVKVGSGAFMPTYE SE LA +I  VANGAG +TTALLT
Sbjct: 181 SLITASILSKKLACSLDALAMDVKVGSGAFMPTYEASEELARSIAAVANGAGTKTTALLT 240

Query: 241 DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGQLAKDDAEARAKL 300
           DMNQVLAS AGNA+EV+EA+ FLTG YRNPRL+ VTM LC EML+ G LA D+A+ARAKL
Sbjct: 241 DMNQVLASCAGNALEVKEAIDFLTGAYRNPRLYAVTMGLCAEMLLLGGLATDEADARAKL 300

Query: 301 QAVLDNGKAAEVFGRMVAAQKGPSDFVENYDKYLPTAMLSKAVYADTEGFISAMDTRALG 360
             VLDNG+AAE+FG+MV+   GP DFVENY KYLP + + + V+ADT+G+  +MDTR LG
Sbjct: 301 NRVLDNGRAAEIFGKMVSGLGGPVDFVENYSKYLPQSQIIRPVFADTQGYAHSMDTRELG 360

Query: 361 MAVVSMGGGRRQASDTIDYSVGFTDMARLGDSIDGQRPLAVIHAKDEASWQEAAKAVKAA 420
           +AVV++GGGRR+  D +DYSVG T +  LGD ID   P+AVIHA+ E ++ +A  AVK A
Sbjct: 361 LAVVTLGGGRRKPGDELDYSVGLTQVCALGDKIDASTPIAVIHAQSEEAFAQAEDAVKKA 420

Query: 421 IILDDKAPASTPSVYRRI 438
           I +D+ AP  TP +Y  I
Sbjct: 421 IHIDEIAPEKTPEIYAYI 438


Lambda     K      H
   0.319    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: 612
Number of extensions: 12
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 200396 SO1218 (thymidine phosphorylase (NCBI ptt file))
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.2605.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   1.5e-222  725.1   4.2   1.7e-222  724.9   4.2    1.0  1  lcl|FitnessBrowser__MR1:200396  SO1218 thymidine phosphorylase (


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:200396  SO1218 thymidine phosphorylase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  724.9   4.2  1.7e-222  1.7e-222       1     437 []       2     438 ..       2     438 .. 1.00

  Alignments for each domain:
  == domain 1  score: 724.9 bits;  conditional E-value: 1.7e-222
                       TIGR02643   1 llpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvldwkdldlngP 79 
                                     +l+qeiirkkr+gl ls+eei+ fv+g+t ++vsegqiaal mavyfn++++de++alt amrdsG+vl+w++l+lngP
  lcl|FitnessBrowser__MR1:200396   2 FLAQEIIRKKRNGLVLSAEEIQFFVKGITTNAVSEGQIAALGMAVYFNDMNMDERIALTTAMRDSGTVLNWQSLNLNGP 80 
                                     79***************************************************************************** PP

                       TIGR02643  80 vvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPdeelfrkvvkdvGvaiiGqtad 158
                                     v+dkhstGGvGdv+slml+P+ aacGgyvPmisGrGlGhtGGtldk++aiPGy++ P++elfrkvvkdvGvaiiGqt+d
  lcl|FitnessBrowser__MR1:200396  81 VIDKHSTGGVGDVISLMLGPMAAACGGYVPMISGRGLGHTGGTLDKFDAIPGYQTEPSSELFRKVVKDVGVAIIGQTGD 159
                                     ******************************************************************************* PP

                       TIGR02643 159 laPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnGafmesleeseelarslvevangaGvrttal 237
                                     l Padkr+y+ird tatvesi+litasilskkla  ldal++dvkvG+Gafm+++e seelars+  vangaG +ttal
  lcl|FitnessBrowser__MR1:200396 160 LVPADKRFYSIRDNTATVESISLITASILSKKLACSLDALAMDVKVGSGAFMPTYEASEELARSIAAVANGAGTKTTAL 238
                                     ******************************************************************************* PP

                       TIGR02643 238 itdmnqalasaaGnavevreavdfltGekrdkrleevtlalaaellvsgklaadeaeaeakleavlesGraaerfarmv 316
                                     +tdmnq+las+aGna+ev+ea+dfltG++r++rl +vt+ l+ae+l+ g+la+dea+a+akl++vl++Graae+f++mv
  lcl|FitnessBrowser__MR1:200396 239 LTDMNQVLASCAGNALEVKEAIDFLTGAYRNPRLYAVTMGLCAEMLLLGGLATDEADARAKLNRVLDNGRAAEIFGKMV 317
                                     ******************************************************************************* PP

                       TIGR02643 317 aalgGPadfvekpekylakaaiakavkaaregylseidtrelGlavvalGGGrrkaddkldlsvGltdllelGekveke 395
                                     + lgGP dfve+++kyl++++i+++v a+++gy +++dtrelGlavv+lGGGrrk+ d+ld+svGlt++  lG+k+++ 
  lcl|FitnessBrowser__MR1:200396 318 SGLGGPVDFVENYSKYLPQSQIIRPVFADTQGYAHSMDTRELGLAVVTLGGGRRKPGDELDYSVGLTQVCALGDKIDAS 396
                                     ******************************************************************************* PP

                       TIGR02643 396 eplavvhaadeedaeeaakavkkalkiadeaPeeakvvleri 437
                                     +p+av+ha++ee +++a +avkka++i++ aPe+++ +++ i
  lcl|FitnessBrowser__MR1:200396 397 TPIAVIHAQSEEAFAQAEDAVKKAIHIDEIAPEKTPEIYAYI 438
                                     ************************************999865 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: 00:00:00.01
# Mc/sec: 10.42
//
[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