Alignments for a candidate for deoA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Cupriavidus basilensis 4G11

Align Putative thymidine phosphorylase; EC 2.4.2.4; TdRPase (uncharacterized)
to candidate RR42_RS21235 RR42_RS21235 thymidine phosphorylase

Query= curated2:Q6N2A3
         (514 letters)



>FitnessBrowser__Cup4G11:RR42_RS21235
          Length = 679

 Score =  380 bits (977), Expect = e-110
 Identities = 209/490 (42%), Positives = 294/490 (60%), Gaps = 9/490 (1%)

Query: 10  PLTIRRISLDTGRENVAVISRRSRALRPEVFRGFSRVELRINSKVLLATLMITDDDAMIG 69
           PL  RR+ + TG  ++A +S       P    G +R+ +R  +  + A L + +  A++ 
Sbjct: 186 PLKARRMPIATGDAHIAYVS-------PAFSAGQTRMAVRSGTVEIPAALHVVESPALLQ 238

Query: 70  PDEVGLSEPAFRRFNEPVGSAVSVTPARSPASLDAVRAKIQGHTLSAAEITAIVDDLAHF 129
            +E+GLS+  F R     GS V +     P S D +R K++G  LS AE  A++ D    
Sbjct: 239 DEEIGLSDALFDRLGAAPGSTVRLRRIPGPVSRDVLRKKLRGDALSEAEYEAVLRDAVEG 298

Query: 130 RYSDMEIAAFLISAARFTTTDELLALVGAMASVGTKLTWDTPIVVDKHCIGGIPGNRTTM 189
           RY+++E+ AFL++A++  T  E++++  A      ++ WD PIVVDKH +GG+PG+R T+
Sbjct: 299 RYTEIELTAFLVAASQHLTDAEVVSVARARTRFAPRIGWDEPIVVDKHSMGGVPGSRITL 358

Query: 190 IVVPIVAAHGLMIPKTSSRAITSPAGTADTMELLARVDLDVEQMKQVVHACGGCLVWGGH 249
           IVVPIVAA GL +PKTSSRAITS AGTA+ ME +ARVDLD++ +++ V     C+ W G 
Sbjct: 359 IVVPIVAAFGLAMPKTSSRAITSAAGTAEAMETVARVDLDIDDVRRCVEQARACIAWNGR 418

Query: 250 VNLSPADDILISVERPLSLDTPEQMVASIMSKKLAAGSTRLLIDFPVGPSAKVTNANEAM 309
           +N S  DD++ ++ RPL LDT    VASI+SKK  AGST +++D P GP AK+ +  EA 
Sbjct: 419 LNHSAIDDVMNAITRPLGLDTNRWSVASILSKKYTAGSTHVIVDLPFGPQAKLKSQAEAQ 478

Query: 310 RLRKLFEFVGDHFGISVEVVTTDGRQPIGRGIGPVLEARDVMAVLGNEPGAPADLREKSL 369
            L  LFE VG   G+ V    T G +PIGRG+GP LE RDV+ VL   P APADLREK+L
Sbjct: 479 ALGVLFEAVGAGLGMQVRAFATHGSKPIGRGVGPALEVRDVLQVLNGSPDAPADLREKAL 538

Query: 370 RLAAHLLEYDPKLRG-GTGYARAKELLDSGAALKKMQQIIDAQGPSPCPAELGSYAADVL 428
             A  +L +DP +     G   A ELL  GAA     +I+ AQG    P   G +   V 
Sbjct: 539 FFAGQILAFDPAVGSPAEGRRMAGELLACGAASAAFDRIVAAQGARAAPDAPGQHVHTVP 598

Query: 429 AAADGVVNGIDCLRINRLARSAGAPVAKGAGIDLFKKIGDRVEKGEPLYRVYASDRSEFD 488
           A+  GVV  I+   I  +AR AGAP   GAG+DL   +GDR+  G+PL+R++A   S+ +
Sbjct: 599 ASTAGVVADINGFAIAGIARGAGAPRRPGAGVDLLCTVGDRLVAGQPLFRIHAQTASDLE 658

Query: 489 LALAA-AQAE 497
             + A A AE
Sbjct: 659 AGVRAHASAE 668


Lambda     K      H
   0.319    0.135    0.386 

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: 915
Number of extensions: 36
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: 514
Length of database: 679
Length adjustment: 37
Effective length of query: 477
Effective length of database: 642
Effective search space:   306234
Effective search space used:   306234
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: 53 (25.0 bits)

Align candidate RR42_RS21235 RR42_RS21235 (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.9436.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-137  445.2   0.3   1.6e-137  444.8   0.3    1.1  1  lcl|FitnessBrowser__Cup4G11:RR42_RS21235  RR42_RS21235 thymidine phosphory


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS21235  RR42_RS21235 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  444.8   0.3  1.6e-137  1.6e-137       3     482 ..     189     663 ..     187     675 .. 0.95

  Alignments for each domain:
  == domain 1  score: 444.8 bits;  conditional E-value: 1.6e-137
                                 TIGR02645   3 vrvlnidtgqekvlinskdlkeekltpqdrvevrlgkkslia..ivvssddlvesgevglseevveele 69 
                                                r++ i tg  ++ ++s+        +q r+ vr+g+ ++ a   vv+s  l++  e+gls  ++++l 
  lcl|FitnessBrowser__Cup4G11:RR42_RS21235 189 ARRMPIATGDAHIAYVSPAFS----AGQTRMAVRSGTVEIPAalHVVESPALLQDEEIGLSDALFDRLG 253
                                               566666666666666655443....5789***********99787889999****************** PP

                                 TIGR02645  70 ekegdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalaingldvdei 138
                                               + +g  v +   + p s +++rkklrg+ l+++e +a+++d v+ +++++e++afl+a     l++ e+
  lcl|FitnessBrowser__Cup4G11:RR42_RS21235 254 AAPGSTVRLRRIPGPVSRDVLRKKLRGDALSEAEYEAVLRDAVEGRYTEIELTAFLVAASQ-HLTDAEV 321
                                               *********************************************************9876.89***** PP

                                 TIGR02645 139 ealtiamvetGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaaGtaDvve 207
                                               + +++a       + wd++++vDkhs+GGvPG +++l+vvpivaa GL +PktssraitsaaGta+ +e
  lcl|FitnessBrowser__Cup4G11:RR42_RS21235 322 VSVARARTRFAPRIGWDEPIVVDKHSMGGVPGSRITLIVVPIVAAFGLAMPKTSSRAITSAAGTAEAME 390
                                               ********************************************************************* PP

                                 TIGR02645 208 vltrvelsveelkrivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskkiaiGstkv 276
                                               +++rv+l +++++r ve+  +c++W G ln +  DDv+  + rpL+lD++   +asilskk+ +Gst+v
  lcl|FitnessBrowser__Cup4G11:RR42_RS21235 391 TVARVDLDIDDVRRCVEQARACIAWNGRLNHSAIDDVMNAITRPLGLDTNRWSVASILSKKYTAGSTHV 459
                                               ********************************************************************* PP

                                 TIGR02645 277 liDiPvGpgakvksvkeaerLakdlielgkrlgvtvevvityGsqPiGraiGPaLeakealavLesske 345
                                               ++D+P Gp ak ks  ea+ L  +++ +g  lg++v    t+Gs+PiGr++GPaLe++++l+vL+ s++
  lcl|FitnessBrowser__Cup4G11:RR42_RS21235 460 IVDLPFGPQAKLKSQAEAQALGVLFEAVGAGLGMQVRAFATHGSKPIGRGVGPALEVRDVLQVLNGSPD 528
                                               ********************************************************************* PP

                                 TIGR02645 346 aPtsLvekslaLaaiLLemggaaer.gaGkelarelLdsGkaleklkeiieaqGgdniksedievGklk 413
                                               aP +L+ek+l  a+ +L +++a+    +G+++a elL+ G+a   + +i+ aqG++   + +   G+  
  lcl|FitnessBrowser__Cup4G11:RR42_RS21235 529 APADLREKALFFAGQILAFDPAVGSpAEGRRMAGELLACGAASAAFDRIVAAQGAR---AAPDAPGQHV 594
                                               *********************9975378***************************9...7777889*** PP

                                 TIGR02645 414 adikaetdGyvteidnkaltriareaGaPedkgaGvklhvkvgdkvkkGdplytiyaeseekldkaial 482
                                                ++ a+t G+v++i+  a++ iar aGaP + gaGv l   vgd+  +G+pl++i+a++ + l+  + +
  lcl|FitnessBrowser__Cup4G11:RR42_RS21235 595 HTVPASTAGVVADINGFAIAGIARGAGAPRRPGAGVDLLCTVGDRLVAGQPLFRIHAQTASDLEAGVRA 663
                                               ***************************************************************998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (679 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: 14.77
//
[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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SQLite3 databases

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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