Alignments for a candidate for deoA in Mesorhizobium ciceri biovar biserrulae WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Mesorhizobium ciceri biovar biserrulae WSM1271

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate WP_013529628.1 MESCI_RS08965 thymidine phosphorylase

Query= BRENDA::Q7CP66
         (440 letters)



>NCBI__GCF_000185905.1:WP_013529628.1
          Length = 439

 Score =  451 bits (1160), Expect = e-131
 Identities = 236/436 (54%), Positives = 305/436 (69%), Gaps = 2/436 (0%)

Query: 3   LAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMA 62
           L QEIIR+KRDG  LS+EEI  F+ G+    +++GQ  A AM +FF+ M   E V+LT+A
Sbjct: 2   LPQEIIRRKRDGLRLSEEEIAGFVAGVTSGAVTDGQAGAFAMAVFFNGMNRDEAVALTLA 61

Query: 63  MRDSGTVLDWKSLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHTGG 122
           MRDSG VLDW   +L GP+ DKHSTGGVGD  SLML P+VAACG YVPMISGRGLGHTGG
Sbjct: 62  MRDSGDVLDWS--DLPGPVTDKHSTGGVGDNVSLMLAPIVAACGAYVPMISGRGLGHTGG 119

Query: 123 TLDKLEAIPGFDIFPDDNRFREIIQDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPL 182
           TLDK++AIPG+   PD   FR+ + + G AIIGQT+ LAPAD+R YA RD++ TV+S+PL
Sbjct: 120 TLDKMDAIPGYISQPDVALFRKAVLETGCAIIGQTADLAPADRRLYAIRDVSGTVESVPL 179

Query: 183 ITGSILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDM 242
           IT SIL+KKLA GL +LV+DVKVG+GAFM     + ALA ++V +ANGAG++ +AL+T M
Sbjct: 180 ITASILSKKLAAGLQSLVLDVKVGNGAFMEKSRDATALANSLVEIANGAGLKASALITGM 239

Query: 243 NQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGQLAKDDAEARAKLQA 302
           N+ LAS+AGNAVEVR AV FLTG YR+ RL DVT+AL  EML    L   + +   +   
Sbjct: 240 NEPLASAAGNAVEVRNAVDFLTGRYRDRRLEDVTLALAAEMLQWAGLVSSNQDGMRRATE 299

Query: 303 VLDNGKAAEVFGRMVAAQKGPSDFVENYDKYLPTAMLSKAVYADTEGFISAMDTRALGMA 362
            L +G+AA  F RMVAA  GP+DF+E  +KYLP A +  AV A   GF+  + TR +G+A
Sbjct: 300 TLASGRAAATFARMVAALGGPADFIEKPEKYLPAAAIELAVKATANGFVIGIATRDVGLA 359

Query: 363 VVSMGGGRRQASDTIDYSVGFTDMARLGDSIDGQRPLAVIHAKDEASWQEAAKAVKAAII 422
           VV +GGGR +  D +D +VG T +  +G  +    PLA++HA+  A  + AA AV +A  
Sbjct: 360 VVGLGGGRTRPDDKVDPAVGITRLLPVGAEVRAGEPLALVHARSLADAEAAADAVLSAYT 419

Query: 423 LDDKAPASTPSVYRRI 438
           +    PA+  SV RRI
Sbjct: 420 VGASKPAADKSVIRRI 435


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: 557
Number of extensions: 31
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: 439
Length adjustment: 32
Effective length of query: 408
Effective length of database: 407
Effective search space:   166056
Effective search space used:   166056
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_013529628.1 MESCI_RS08965 (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.1760550.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   3.9e-224  730.3  13.0   4.4e-224  730.2  13.0    1.0  1  NCBI__GCF_000185905.1:WP_013529628.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000185905.1:WP_013529628.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  730.2  13.0  4.4e-224  4.4e-224       1     437 []       1     435 [.       1     435 [. 1.00

  Alignments for each domain:
  == domain 1  score: 730.2 bits;  conditional E-value: 4.4e-224
                             TIGR02643   1 llpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvldwkd 73 
                                           +lpqeiir+krdgl+ls+eeia fv+gvt+++v++gq+ a+amav+fng+++de+valtlamrdsGdvldw+ 
  NCBI__GCF_000185905.1:WP_013529628.1   1 MLPQEIIRRKRDGLRLSEEEIAGFVAGVTSGAVTDGQAGAFAMAVFFNGMNRDEAVALTLAMRDSGDVLDWS- 72 
                                           89**********************************************************************. PP

                             TIGR02643  74 ldlngPvvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPdeelfrkvvk 146
                                            dl+gPv+dkhstGGvGd+vslmlaPivaacG+yvPmisGrGlGhtGGtldk++aiPGy ++Pd +lfrk+v 
  NCBI__GCF_000185905.1:WP_013529628.1  73 -DLPGPVTDKHSTGGVGDNVSLMLAPIVAACGAYVPMISGRGLGHTGGTLDKMDAIPGYISQPDVALFRKAVL 144
                                           .************************************************************************ PP

                             TIGR02643 147 dvGvaiiGqtadlaPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnGafmesleeseel 219
                                           ++G+aiiGqtadlaPad+rlyairdv++tves+plitasilskklaaGl++lvldvkvGnGafme+++++++l
  NCBI__GCF_000185905.1:WP_013529628.1 145 ETGCAIIGQTADLAPADRRLYAIRDVSGTVESVPLITASILSKKLAAGLQSLVLDVKVGNGAFMEKSRDATAL 217
                                           ************************************************************************* PP

                             TIGR02643 220 arslvevangaGvrttalitdmnqalasaaGnavevreavdfltGekrdkrleevtlalaaellvsgklaade 292
                                           a+slve+angaG++++alit mn++lasaaGnavevr+avdfltG++rd+rle+vtlalaae+l+ ++l++++
  NCBI__GCF_000185905.1:WP_013529628.1 218 ANSLVEIANGAGLKASALITGMNEPLASAAGNAVEVRNAVDFLTGRYRDRRLEDVTLALAAEMLQWAGLVSSN 290
                                           ************************************************************************* PP

                             TIGR02643 293 aeaeakleavlesGraaerfarmvaalgGPadfvekpekylakaaiakavkaaregylseidtrelGlavval 365
                                           +++ ++++++l sGraa++farmvaalgGPadf+ekpekyl+ aai++avka+++g++  i+tr++Glavv+l
  NCBI__GCF_000185905.1:WP_013529628.1 291 QDGMRRATETLASGRAAATFARMVAALGGPADFIEKPEKYLPAAAIELAVKATANGFVIGIATRDVGLAVVGL 363
                                           ************************************************************************* PP

                             TIGR02643 366 GGGrrkaddkldlsvGltdllelGekvekeeplavvhaadeedaeeaakavkkalkiadeaPeeakvvleri 437
                                           GGGr+++ddk+d++vG+t+ll++G++v ++epla+vha++ +dae+aa+av +a+++++++P+++k+v++ri
  NCBI__GCF_000185905.1:WP_013529628.1 364 GGGRTRPDDKVDPAVGITRLLPVGAEVRAGEPLALVHARSLADAEAAADAVLSAYTVGASKPAADKSVIRRI 435
                                           ********************************************************************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (437 nodes)
Target sequences:                          1  (439 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 19.13
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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