Alignments for a candidate for deoA in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Pseudomonas stutzeri RCH2

Align Putative thymidine phosphorylase; EC 2.4.2.4; TdRPase (uncharacterized)
to candidate GFF3458 Psest_3523 putative thymidine phosphorylase

Query= curated2:Q21W90
         (522 letters)



>FitnessBrowser__psRCH2:GFF3458
          Length = 526

 Score =  774 bits (1999), Expect = 0.0
 Identities = 390/509 (76%), Positives = 445/509 (87%)

Query: 14  LVLRRVAIDTYRENVAYLHRDCAVYRAEGFQALSKVEVRANGRHILATLNVVDDPNIVAC 73
           L LRRVAIDTYRENVAYLHRDCA  RAEGFQAL+KVE+R NG+ ILA+LN+VDDP IV C
Sbjct: 18  LALRRVAIDTYRENVAYLHRDCAACRAEGFQALAKVEIRVNGKRILASLNLVDDPAIVGC 77

Query: 74  NELGLSEDAFAQMAVIDGQPASVSQAEPPQSIGALRRKLAGERLGREDFLGIVRDIAELH 133
           +ELGLSEDAFAQ+    G PAS+SQAEP  SI AL RK+AGERL REDFL I+RDIAE  
Sbjct: 78  DELGLSEDAFAQLGAEAGVPASISQAEPAASIPALHRKIAGERLRREDFLAIMRDIAEHR 137

Query: 134 YSKIELSAFVVATNRDELDREEVYFLTEAMVASGRTLNWHEPLVVDKHCIGGIPGNRSSM 193
           YSKIEL+AFVVA N+ ELDREEV+FLT+AM+  GR L+W E  VVDKHCIGGIPGNR+SM
Sbjct: 138 YSKIELTAFVVACNQGELDREEVFFLTDAMIQVGRRLDWREHPVVDKHCIGGIPGNRTSM 197

Query: 194 LVVPIVAAHGLLCPKTSSRAITSPAGTADTMEVLAKVELPVDQLADIVRTHRGCLAWGGA 253
           LVVPIVAAHG+LCPKTSSRAITSPAGTADTMEVLA VELP ++L ++VR  RGCLAWGG 
Sbjct: 198 LVVPIVAAHGMLCPKTSSRAITSPAGTADTMEVLANVELPFERLCEMVREERGCLAWGGT 257

Query: 254 AHLSPADDVLISVERPLAIDSPGQMVASILSKKIAAGSTHLVLDIPIGPSAKVRSMPEAQ 313
           + LSPADDVLI+VERPL+IDSPGQMVASILSKKIAAGSTHL+LDIPIGP+AKVRSM EAQ
Sbjct: 258 SELSPADDVLIAVERPLSIDSPGQMVASILSKKIAAGSTHLLLDIPIGPTAKVRSMAEAQ 317

Query: 314 RLRRLFEYVAGRMHLSLDVVVTDGRQPIGNGIGPVLEARDVMRVLENDPRAPNDLRQKSL 373
           RLR+LFE+VA R+ L+LDVV+TDGRQPIGNGIGPVLEARDVM+VL+NDP AP DLRQK+L
Sbjct: 318 RLRKLFEFVASRLGLTLDVVITDGRQPIGNGIGPVLEARDVMQVLQNDPAAPIDLRQKAL 377

Query: 374 RLAGRLIEFDPDVRGGDGFAIARDILDSGRALAKMNAIIAAQGAKPFDHNHPQLGALTFD 433
           RLAGR++EFDPDVRGGDG+AIARDILDSGRAL KM++IIAAQG+KPFDHNHP L  L+FD
Sbjct: 378 RLAGRMLEFDPDVRGGDGYAIARDILDSGRALKKMHSIIAAQGSKPFDHNHPPLARLSFD 437

Query: 434 ICASESGVVTGIDNLQVARIARLAGAPKVIGAGIDLFHKLGEAVTSGEVLYRVHAGFQSD 493
           + A  S VVTGIDNLQ+ARIARLAGAPKV GAG+D+  KLGE V +G+ LYRV+A F +D
Sbjct: 438 VLAERSAVVTGIDNLQLARIARLAGAPKVQGAGVDILRKLGEPVQAGDCLYRVYADFPAD 497

Query: 494 LDFARQACAKSTGYTLGRAEDVPHVFTEF 522
           L FARQA  +++G +LG A+ VP VF EF
Sbjct: 498 LAFARQATERASGVSLGSADQVPSVFVEF 526


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: 912
Number of extensions: 30
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: 522
Length of database: 526
Length adjustment: 35
Effective length of query: 487
Effective length of database: 491
Effective search space:   239117
Effective search space used:   239117
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 GFF3458 Psest_3523 (putative 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.8866.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     1e-187  610.4   0.0   1.3e-187  610.1   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3458  Psest_3523 putative thymidine ph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3458  Psest_3523 putative thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  610.1   0.0  1.3e-187  1.3e-187       2     489 ..      19     511 ..      18     514 .. 0.98

  Alignments for each domain:
  == domain 1  score: 610.1 bits;  conditional E-value: 1.3e-187
                           TIGR02645   2 kvrvlnidtgqekvlinskd...lkeekltpqdrvevrlgkkslia..ivvssddlvesgevglseevveeleek 71 
                                          +r++ idt +e+v + ++d   +++e++++ ++ve+r+++k ++a  ++v++  +v  +e+glse+++ +l ++
  lcl|FitnessBrowser__psRCH2:GFF3458  19 ALRRVAIDTYRENVAYLHRDcaaCRAEGFQALAKVEIRVNGKRILAslNLVDDPAIVGCDELGLSEDAFAQLGAE 93 
                                         689*****************9999**********************887888889******************** PP

                           TIGR02645  72 egdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalaingldvdeiealtiamv 146
                                          g   ++++ae++ s++a+++k+ g++l++e+  ai++di+++++s +e++af++a++ + ld +e+  lt am+
  lcl|FitnessBrowser__psRCH2:GFF3458  94 AGVPASISQAEPAASIPALHRKIAGERLRREDFLAIMRDIAEHRYSKIELTAFVVACNQGELDREEVFFLTDAMI 168
                                         *************************************************************************** PP

                           TIGR02645 147 etGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaaGtaDvvevltrvelsveelkr 221
                                         + G  l+w ++++vDkh+iGG+PGn+ts+lvvpivaa+G+l Pktssraits+aGtaD++evl++vel  e l +
  lcl|FitnessBrowser__psRCH2:GFF3458 169 QVGRRLDWREHPVVDKHCIGGIPGNRTSMLVVPIVAAHGMLCPKTSSRAITSPAGTADTMEVLANVELPFERLCE 243
                                         *************************************************************************** PP

                           TIGR02645 222 ivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskkiaiGstkvliDiPvGpgakvksvkeaer 296
                                         +v +  gcl+WGG  +l+PaDDvli verpLs+D+  q++asilskkia+Gst++l+DiP+Gp+akv+s+ ea+r
  lcl|FitnessBrowser__psRCH2:GFF3458 244 MVREERGCLAWGGTSELSPADDVLIAVERPLSIDSPGQMVASILSKKIAAGSTHLLLDIPIGPTAKVRSMAEAQR 318
                                         *************************************************************************** PP

                           TIGR02645 297 LakdlielgkrlgvtvevvityGsqPiGraiGPaLeakealavLesskeaPtsLvekslaLaaiLLemggaaerg 371
                                         L+k+++++++rlg t +vvit+G+qPiG++iGP+Lea+++++vL+++++aP +L+ k+l+La+ +Le+++ ++ g
  lcl|FitnessBrowser__psRCH2:GFF3458 319 LRKLFEFVASRLGLTLDVVITDGRQPIGNGIGPVLEARDVMQVLQNDPAAPIDLRQKALRLAGRMLEFDPDVRGG 393
                                         *************************************************************************** PP

                           TIGR02645 372 aGkelarelLdsGkaleklkeiieaqGgdniksedievGklkadikaetdGyvteidnkaltriareaGaPedkg 446
                                          G+++ar++LdsG+al+k++ ii aqG++  ++++ ++ +l++d+ ae++ +vt idn +l+riar+aGaP+ +g
  lcl|FitnessBrowser__psRCH2:GFF3458 394 DGYAIARDILDSGRALKKMHSIIAAQGSKPFDHNHPPLARLSFDVLAERSAVVTGIDNLQLARIARLAGAPKVQG 468
                                         *************************************************************************** PP

                           TIGR02645 447 aGvklhvkvgdkvkkGdplytiyaeseekldkaialaralepi 489
                                         aGv + +k+g+ v++Gd ly++ya+    l  a ++ ++ +++
  lcl|FitnessBrowser__psRCH2:GFF3458 469 AGVDILRKLGEPVQAGDCLYRVYADFPADLAFARQATERASGV 511
                                         ************************9998888887777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (526 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 9.94
//
[ok]

This GapMind analysis is from Sep 17 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