Alignments for a candidate for deoA in Rhizobium leguminosarum 3841

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Rhizobium leguminosarum 3841

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate WP_011650015.1 RL_RS01075 thymidine phosphorylase

Query= BRENDA::Q7CP66
         (440 letters)



>NCBI__GCF_000009265.1:WP_011650015.1
          Length = 435

 Score =  437 bits (1124), Expect = e-127
 Identities = 227/432 (52%), Positives = 301/432 (69%), Gaps = 2/432 (0%)

Query: 3   LAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMA 62
           + QEIIR+KRDG  L   EI  FI  +    +SEGQI A AM ++F  M+  E V+LT+A
Sbjct: 2   IPQEIIRRKRDGDELDAAEISSFIAALAAGQLSEGQIGAFAMAVWFKGMSRTETVALTLA 61

Query: 63  MRDSGTVLDWKSLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHTGG 122
           M DSG  L W   +++ PI DKHSTGGVGD  SLML P+ AACG  VPMISGRGLGHTGG
Sbjct: 62  MADSGDRLQWA--DVDRPIADKHSTGGVGDNVSLMLAPIAAACGLAVPMISGRGLGHTGG 119

Query: 123 TLDKLEAIPGFDIFPDDNRFREIIQDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPL 182
           TLDKLE+IPG+ I PD + F +++++ G AIIGQT +LAPAD R YA RD+TATVDSIPL
Sbjct: 120 TLDKLESIPGYMITPDADLFHKVVKEAGCAIIGQTGTLAPADGRLYAVRDVTATVDSIPL 179

Query: 183 ITGSILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDM 242
           IT SIL+KKLA GL+ LV+DVKVG+GAFM     +E LA+++V VANGAGV+T+AL+TDM
Sbjct: 180 ITASILSKKLAAGLETLVLDVKVGNGAFMVDRGQAETLAQSLVEVANGAGVKTSALITDM 239

Query: 243 NQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGQLAKDDAEARAKLQA 302
           NQ LA SAGNAVE+R  + FL G   + RL  V +A   EML+   +A    EA    + 
Sbjct: 240 NQPLADSAGNAVEMRNCLDFLAGRKADTRLETVVLAFAAEMLVKSGIAASSDEAEGMARR 299

Query: 303 VLDNGKAAEVFGRMVAAQKGPSDFVENYDKYLPTAMLSKAVYADTEGFISAMDTRALGMA 362
            L +GKAAEVF RMV+   GP+D +EN D+YL  A ++K V A   G+++A D R +G++
Sbjct: 300 ALSSGKAAEVFARMVSMLGGPADLIENPDRYLARAPVAKPVPAARSGWLAACDARGIGVS 359

Query: 363 VVSMGGGRRQASDTIDYSVGFTDMARLGDSIDGQRPLAVIHAKDEASWQEAAKAVKAAII 422
           V+ +GGGRR  +D ID+ VGF+++  LG  ++   P+A++HA D+A+ + A  A+ A   
Sbjct: 360 VIDLGGGRRHPADRIDHRVGFSELLPLGTRVNAGEPIALVHAADDAAAERAVAALAAHYR 419

Query: 423 LDDKAPASTPSV 434
           + ++ P  TP +
Sbjct: 420 ITEEKPELTPVI 431


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: 530
Number of extensions: 16
Number of successful extensions: 2
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: 435
Length adjustment: 32
Effective length of query: 408
Effective length of database: 403
Effective search space:   164424
Effective search space used:   164424
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 WP_011650015.1 RL_RS01075 (thymidine phosphorylase)
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.8718.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     1e-215  702.6  11.3   1.2e-215  702.4  11.3    1.0  1  lcl|NCBI__GCF_000009265.1:WP_011650015.1  RL_RS01075 thymidine phosphoryla


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000009265.1:WP_011650015.1  RL_RS01075 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  702.4  11.3  1.2e-215  1.2e-215       1     434 [.       1     432 [.       1     435 [] 0.99

  Alignments for each domain:
  == domain 1  score: 702.4 bits;  conditional E-value: 1.2e-215
                                 TIGR02643   1 llpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvl 69 
                                               ++pqeiir+krdg++l+++ei +f+++++++++segqi a+amav+f+g+++ e+valtlam dsGd+l
  lcl|NCBI__GCF_000009265.1:WP_011650015.1   1 MIPQEIIRRKRDGDELDAAEISSFIAALAAGQLSEGQIGAFAMAVWFKGMSRTETVALTLAMADSGDRL 69 
                                               79******************************************************************* PP

                                 TIGR02643  70 dwkdldlngPvvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPde 138
                                               +w   d+++P++dkhstGGvGd+vslmlaPi aacG +vPmisGrGlGhtGGtldkle+iPGy ++Pd 
  lcl|NCBI__GCF_000009265.1:WP_011650015.1  70 QWA--DVDRPIADKHSTGGVGDNVSLMLAPIAAACGLAVPMISGRGLGHTGGTLDKLESIPGYMITPDA 136
                                               ***..99************************************************************** PP

                                 TIGR02643 139 elfrkvvkdvGvaiiGqtadlaPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnG 207
                                               +lf kvvk++G+aiiGqt+ laPad rlya+rdvtatv+siplitasilskklaaGl++lvldvkvGnG
  lcl|NCBI__GCF_000009265.1:WP_011650015.1 137 DLFHKVVKEAGCAIIGQTGTLAPADGRLYAVRDVTATVDSIPLITASILSKKLAAGLETLVLDVKVGNG 205
                                               ********************************************************************* PP

                                 TIGR02643 208 afmesleeseelarslvevangaGvrttalitdmnqalasaaGnavevreavdfltGekrdkrleevtl 276
                                               afm +  ++e+la+slvevangaGv+t+alitdmnq+la++aGnave+r+++dfl+G+k+d+rle v+l
  lcl|NCBI__GCF_000009265.1:WP_011650015.1 206 AFMVDRGQAETLAQSLVEVANGAGVKTSALITDMNQPLADSAGNAVEMRNCLDFLAGRKADTRLETVVL 274
                                               ********************************************************************* PP

                                 TIGR02643 277 alaaellvsgklaadeaeaeakleavlesGraaerfarmvaalgGPadfvekpekylakaaiakavkaa 345
                                               a+aae+lv++++aa+++eae +++++l+sG+aae+farmv++lgGPad++e+p++yla+a++ak+v+aa
  lcl|NCBI__GCF_000009265.1:WP_011650015.1 275 AFAAEMLVKSGIAASSDEAEGMARRALSSGKAAEVFARMVSMLGGPADLIENPDRYLARAPVAKPVPAA 343
                                               ********************************************************************* PP

                                 TIGR02643 346 regylseidtrelGlavvalGGGrrkaddkldlsvGltdllelGekvekeeplavvhaadeedaeeaak 414
                                               r+g+l+++d+r +G++v+ lGGGrr++ d++d++vG+++ll+lG++v+++ep+a+vhaad++ ae+a++
  lcl|NCBI__GCF_000009265.1:WP_011650015.1 344 RSGWLAACDARGIGVSVIDLGGGRRHPADRIDHRVGFSELLPLGTRVNAGEPIALVHAADDAAAERAVA 412
                                               ********************************************************************* PP

                                 TIGR02643 415 avkkalkiadeaPeeakvvl 434
                                               a+ + ++i++e+Pe ++v+ 
  lcl|NCBI__GCF_000009265.1:WP_011650015.1 413 ALAAHYRITEEKPELTPVIA 432
                                               ****************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (437 nodes)
Target sequences:                          1  (435 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: 6.89
//
[ok]

This GapMind analysis is from Sep 24 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