Alignments for a candidate for deoA in Methylococcus capsulatus Bath

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Methylococcus capsulatus Bath

Align Putative thymidine phosphorylase; EC 2.4.2.4; TdRPase (uncharacterized)
to candidate WP_010960971.1 MCA_RS08450 thymidine phosphorylase

Query= curated2:Q21W90
         (522 letters)



>NCBI__GCF_000008325.1:WP_010960971.1
          Length = 516

 Score =  622 bits (1605), Expect = 0.0
 Identities = 320/518 (61%), Positives = 398/518 (76%), Gaps = 3/518 (0%)

Query: 5   TDKPQLASKLVLRRVAIDTYRENVAYLHRDCAVYRAEGFQALSKVEVRANGRHILATLNV 64
           +D+  + ++L LR VAIDTYRENVAYLHR+C+VYRAEGFQAL+K+ V  NG+ I A LNV
Sbjct: 2   SDEESIKTRLKLRPVAIDTYRENVAYLHRECSVYRAEGFQALAKIRVGCNGKQIEAVLNV 61

Query: 65  VDDPNIVACNELGLSEDAFAQMAVIDGQPASVSQAEPPQSIGALRRKLAGERLGREDFLG 124
           VDD  IVA +ELGLSE AF +     GQ  +V+QAEPP S+  +RRK+ GERL   D+  
Sbjct: 62  VDDVCIVAPDELGLSEQAFQRFGEPAGQLVNVAQAEPPLSMDGVRRKIGGERLDYGDYQA 121

Query: 125 IVRDIAELHYSKIELSAFVVATNRDELDREEVYFLTEAMVASGRTLNWHEPLVVDKHCIG 184
           I  DIA+  YSK+E++AF+VAT ++ LDR+EV  LT AM+ +G  L+W+EPLV DKHCIG
Sbjct: 122 ITSDIAKGRYSKMEMAAFLVATGQNGLDRDEVLSLTRAMLETGVRLSWNEPLVADKHCIG 181

Query: 185 GIPGNRSSMLVVPIVAAHGLLCPKTSSRAITSPAGTADTMEVLAKVELPVDQLADIVRTH 244
           GIPGNR+S+L+VPIVAAHG+L PKTSSRAITSPAGTADTMEVLA+ +L  + L  +VR  
Sbjct: 182 GIPGNRTSLLIVPIVAAHGMLIPKTSSRAITSPAGTADTMEVLARTDLAPESLDRLVRME 241

Query: 245 RGCLAWGGAAHLSPADDVLISVERPLAIDSPGQMVASILSKKIAAGSTHLVLDIPIGPSA 304
           RGCLAWGG   L+P DD+LISVERPL IDS GQMVASILSKK+AAG+THL+LDIP+GP+A
Sbjct: 242 RGCLAWGGTTRLAPVDDMLISVERPLGIDSQGQMVASILSKKLAAGATHLLLDIPVGPTA 301

Query: 305 KVRSMPEAQRLRRLFEYVAGRMHLSLDVVVTDGRQPIGNGIGPVLEARDVMRVLENDPRA 364
           KVR M +A  LR+LFEYV  R+ L L+ V+TDG QP+G GIGPVLE RDVM+VLENDP A
Sbjct: 302 KVRQMRDAMSLRKLFEYVGDRVGLHLEAVITDGAQPVGRGIGPVLEVRDVMQVLENDPEA 361

Query: 365 PNDLRQKSLRLAGRLIEFDPDVRGGDGFAIARDILDSGRALAKMNAIIAAQGAKPFDHNH 424
           P DLR+KSLRLAGR++EFDPDVRGG G++IARDIL+SGRALAKM+ II AQG +      
Sbjct: 362 PVDLREKSLRLAGRILEFDPDVRGGFGYSIARDILESGRALAKMHRIIDAQGRQ---ERR 418

Query: 425 PQLGALTFDICASESGVVTGIDNLQVARIARLAGAPKVIGAGIDLFHKLGEAVTSGEVLY 484
            + G L F++ A  +GVV GIDN  +A+ ARLAGAP   GAG+DL +KLG+ V  G+ LY
Sbjct: 419 LEPGRLVFEVRAERAGVVVGIDNFFLAQTARLAGAPMSRGAGVDLLNKLGDTVEEGQPLY 478

Query: 485 RVHAGFQSDLDFARQACAKSTGYTLGRAEDVPHVFTEF 522
           RV+A F ++ +FAR+     +GY +G A  +     EF
Sbjct: 479 RVYAEFPANFEFAREFTRTRSGYNIGDAAFLTKTHMEF 516


Lambda     K      H
   0.320    0.137    0.396 

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: 788
Number of extensions: 29
Number of successful extensions: 3
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: 522
Length of database: 516
Length adjustment: 35
Effective length of query: 487
Effective length of database: 481
Effective search space:   234247
Effective search space used:   234247
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 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_010960971.1 MCA_RS08450 (thymidine phosphorylase)
to HMM TIGR02645 (putative 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/TIGR02645.hmm
# target sequence database:        /tmp/gapView.18590.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02645  [M=493]
Accession:   TIGR02645
Description: ARCH_P_rylase: putative 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.4e-186  604.1   0.0   9.5e-186  603.9   0.0    1.0  1  lcl|NCBI__GCF_000008325.1:WP_010960971.1  MCA_RS08450 thymidine phosphoryl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010960971.1  MCA_RS08450 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  603.9   0.0  9.5e-186  9.5e-186       1     491 [.      11     503 ..      11     505 .. 0.98

  Alignments for each domain:
  == domain 1  score: 603.9 bits;  conditional E-value: 9.5e-186
                                 TIGR02645   1 lkvrvlnidtgqekvlinskd...lkeekltpqdrvevrlgkkslia..ivvssddlvesgevglseev 64 
                                               lk+r++ idt +e+v + +++    ++e++++ ++++v  ++k++ a  +vv++  +v+ +e+glse++
  lcl|NCBI__GCF_000008325.1:WP_010960971.1  11 LKLRPVAIDTYRENVAYLHREcsvYRAEGFQALAKIRVGCNGKQIEAvlNVVDDVCIVAPDELGLSEQA 79 
                                               79*******************77779*********************7777778889************ PP

                                 TIGR02645  65 veeleekegdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalaingl 133
                                               ++++ e+ g+lv+v +ae+p s++ +r+k+ g++l+  + +ai sdi++ ++s +e++afl+a+  ngl
  lcl|NCBI__GCF_000008325.1:WP_010960971.1  80 FQRFGEPAGQLVNVAQAEPPLSMDGVRRKIGGERLDYGDYQAITSDIAKGRYSKMEMAAFLVATGQNGL 148
                                               ********************************************************************* PP

                                 TIGR02645 134 dvdeiealtiamvetGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaaGt 202
                                               d de++ lt+am etG  l+w+++ ++Dkh+iGG+PGn+tsll+vpivaa+G+liPktssraits+aGt
  lcl|NCBI__GCF_000008325.1:WP_010960971.1 149 DRDEVLSLTRAMLETGVRLSWNEPLVADKHCIGGIPGNRTSLLIVPIVAAHGMLIPKTSSRAITSPAGT 217
                                               ********************************************************************* PP

                                 TIGR02645 203 aDvvevltrvelsveelkrivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskkiai 271
                                               aD++evl+r +l+ e l r+v    gcl+WGG + laP DD+li+verpL++D++ q++asilskk+a+
  lcl|NCBI__GCF_000008325.1:WP_010960971.1 218 ADTMEVLARTDLAPESLDRLVRMERGCLAWGGTTRLAPVDDMLISVERPLGIDSQGQMVASILSKKLAA 286
                                               ********************************************************************* PP

                                 TIGR02645 272 GstkvliDiPvGpgakvksvkeaerLakdlielgkrlgvtvevvityGsqPiGraiGPaLeakealavL 340
                                               G+t++l+DiPvGp+akv+ +++a++L+k+++ +g+r+g + e vit+G+qP+Gr+iGP+Le++++++vL
  lcl|NCBI__GCF_000008325.1:WP_010960971.1 287 GATHLLLDIPVGPTAKVRQMRDAMSLRKLFEYVGDRVGLHLEAVITDGAQPVGRGIGPVLEVRDVMQVL 355
                                               ********************************************************************* PP

                                 TIGR02645 341 esskeaPtsLvekslaLaaiLLemggaaergaGkelarelLdsGkaleklkeiieaqGgdniksediev 409
                                               e+++eaP +L+eksl+La+ +Le+++ ++ g G+ +ar++L+sG+al k+++ii+aqG +   +   e 
  lcl|NCBI__GCF_000008325.1:WP_010960971.1 356 ENDPEAPVDLREKSLRLAGRILEFDPDVRGGFGYSIARDILESGRALAKMHRIIDAQGRQ---ERRLEP 421
                                               ***********************************************************9...889999 PP

                                 TIGR02645 410 GklkadikaetdGyvteidnkaltriareaGaPedkgaGvklhvkvgdkvkkGdplytiyaeseekldk 478
                                               G+l +++ ae+ G+v  idn  l++ ar+aGaP+ +gaGv l  k+gd v++G+ply++yae   +++ 
  lcl|NCBI__GCF_000008325.1:WP_010960971.1 422 GRLVFEVRAERAGVVVGIDNFFLAQTARLAGAPMSRGAGVDLLNKLGDTVEEGQPLYRVYAEFPANFEF 490
                                               **************************************************************9999999 PP

                                 TIGR02645 479 aialaralepikv 491
                                               a +  r+ +++++
  lcl|NCBI__GCF_000008325.1:WP_010960971.1 491 AREFTRTRSGYNI 503
                                               9888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (516 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: 12.15
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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