Alignments for a candidate for deoA in Methanococcus aeolicus Nankai-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Methanococcus aeolicus Nankai-3

Align Putative thymidine phosphorylase; EC 2.4.2.4; TdRPase (uncharacterized)
to candidate WP_011973334.1 MAEO_RS03075 AMP phosphorylase

Query= curated2:Q6N2A3
         (514 letters)



>NCBI__GCF_000017185.1:WP_011973334.1
          Length = 504

 Score =  342 bits (876), Expect = 2e-98
 Identities = 196/458 (42%), Positives = 276/458 (60%), Gaps = 7/458 (1%)

Query: 43  FSRVELRINSKVLLATLMITDDDAMIGPDEVGLSEPAFR-RFNEPVGSAVSVTPARSPAS 101
           +S+  + I SK       +     MI P EVG+S+     + NE  G  V V  A+ P S
Sbjct: 31  YSQDRVLIESKTCSFIGTLQSTKTMIKPGEVGVSKYIKDVKLNE--GEEVRVRHAQKPQS 88

Query: 102 LDAVRAKIQGHTLSAAEITAIVDDLAHFRYSDMEIAAFLISA-ARFTTTDELLALVGAMA 160
           +  +R K+ G TL+A EI  I+D++   + +++E++AFL+S   R   T+E++A+   MA
Sbjct: 89  VSYIRKKMNGQTLTADEIHTIIDEIVSKKLTNVELSAFLVSTYIRGMNTEEIVAMTKRMA 148

Query: 161 SVGTKLTWDTPIVVDKHCIGGIPGNRTTMIVVPIVAAHGLMIPKTSSRAITSPAGTADTM 220
             G  + W+   VVD H IGG+PGN+  ++ +PIVAA G+ IPKTSSRAITS AGTAD +
Sbjct: 149 ETGDTIQWEKRPVVDVHSIGGVPGNKYALLTIPIVAAAGMTIPKTSSRAITSAAGTADVL 208

Query: 221 ELLARVDLDVEQMKQVVHACGGCLVWGGHVNLSPADDILISVERPLSLDTPEQMVASIMS 280
           E++  V+L  E++++V    GGCL WGG VNL+PADDI+I+VERPLS+D   Q++AS+M+
Sbjct: 209 EVITNVNLSCEEIQRVAKTTGGCLAWGGAVNLAPADDIIINVERPLSIDPQPQLLASVMA 268

Query: 281 KKLAAGSTRLLIDFPVGPSAKVTNANEAMRLRKLFEFVGDHFGISVEVVTTDGRQPIGRG 340
           KK+A G    +ID PVG   K+ N  E  +L + F  +G+  GI VE V T G QPIGR 
Sbjct: 269 KKIATGIDYTVIDIPVGYGVKIKNEKEGNQLARKFIELGELLGIRVECVLTYGGQPIGRA 328

Query: 341 IGPVLEARDVMAVLGNEPGAPADLREKSLRLAAHLLEYDPKLRGGTGYARAKELLDSGAA 400
           IGP LE ++ +  L +   AP  L EKS+ LA  LLE   + + G G   A E+L+SG A
Sbjct: 329 IGPALEIKEALMALHDPKSAPNSLIEKSVSLAGVLLELGGRAQIGQGQKVAWEILESGKA 388

Query: 401 LKKMQQIIDAQG---PSPCPAELGSYAADVLAAADGVVNGIDCLRINRLARSAGAPVAKG 457
           L+K  +I+  QG     P   ELG Y  D+ +  DG V GI    I +LA+ AG P  K 
Sbjct: 389 LEKFNEIVVEQGGTITKPEEIELGEYTMDIRSPKDGYVTGISNKLITKLAKEAGCPKDKK 448

Query: 458 AGIDLFKKIGDRVEKGEPLYRVYASDRSEFDLALAAAQ 495
           AGI L  K G++V K + LY +Y+S     D A+  A+
Sbjct: 449 AGIFLGVKTGNKVNKEDILYTIYSSSEERLDAAVNFAR 486


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: 538
Number of extensions: 24
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: 504
Length adjustment: 34
Effective length of query: 480
Effective length of database: 470
Effective search space:   225600
Effective search space used:   225600
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_011973334.1 MAEO_RS03075 (AMP 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.2873405.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.5e-210  683.2   8.2   9.6e-210  683.0   8.2    1.0  1  NCBI__GCF_000017185.1:WP_011973334.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000017185.1:WP_011973334.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  683.0   8.2  9.6e-210  9.6e-210       1     493 []       4     495 ..       4     495 .. 0.99

  Alignments for each domain:
  == domain 1  score: 683.0 bits;  conditional E-value: 9.6e-210
                             TIGR02645   1 lkvrvlnidtgqekvlinskdlkeekltpqdrvevrlgkksliaivvssddlvesgevglseevveeleekeg 73 
                                           l+v+ l++d++ + v+in++d+k + + +qdrv +++++ s i++++s++++++ gevg+s+  ++  + +eg
  NCBI__GCF_000017185.1:WP_011973334.1   4 LEVKFLDLDLEANAVIINEEDIKGTAYYSQDRVLIESKTCSFIGTLQSTKTMIKPGEVGVSKY-IKDVKLNEG 75 
                                           57999*******************************************************976.578899999 PP

                             TIGR02645  74 dlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalaingldvdeiealtiamv 146
                                           + v v +a+kp+s+++irkk++g++l+ +ei++i+++iv +kl++ve+safl++++i g++++ei+a+t++m+
  NCBI__GCF_000017185.1:WP_011973334.1  76 EEVRVRHAQKPQSVSYIRKKMNGQTLTADEIHTIIDEIVSKKLTNVELSAFLVSTYIRGMNTEEIVAMTKRMA 148
                                           99*********************************************************************** PP

                             TIGR02645 147 etGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaaGtaDvvevltrvelsveel 219
                                           etG+t++w+++++vD+hsiGGvPGnk++ll +pivaaaG++iPktssraitsaaGtaDv+ev+t+v+ls ee+
  NCBI__GCF_000017185.1:WP_011973334.1 149 ETGDTIQWEKRPVVDVHSIGGVPGNKYALLTIPIVAAAGMTIPKTSSRAITSAAGTADVLEVITNVNLSCEEI 221
                                           ************************************************************************* PP

                             TIGR02645 220 krivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskkiaiGstkvliDiPvGpgakvksvk 292
                                           +r+ + +ggcl+WGGa+nlaPaDD++i+verpLs+Dp+ qllas+++kkia G ++ +iDiPvG+g k+k  k
  NCBI__GCF_000017185.1:WP_011973334.1 222 QRVAKTTGGCLAWGGAVNLAPADDIIINVERPLSIDPQPQLLASVMAKKIATGIDYTVIDIPVGYGVKIKNEK 294
                                           ************************************************************************* PP

                             TIGR02645 293 eaerLakdlielgkrlgvtvevvityGsqPiGraiGPaLeakealavLesskeaPtsLvekslaLaaiLLemg 365
                                           e+++La+++ielg+ lg++ve+v tyG+qPiGraiGPaLe+keal +L++ k+aP+sL+eks++La++LLe+g
  NCBI__GCF_000017185.1:WP_011973334.1 295 EGNQLARKFIELGELLGIRVECVLTYGGQPIGRAIGPALEIKEALMALHDPKSAPNSLIEKSVSLAGVLLELG 367
                                           ************************************************************************* PP

                             TIGR02645 366 gaaergaGkelarelLdsGkaleklkeiieaqGgdniksedievGklkadikaetdGyvteidnkaltriare 438
                                           g a+ g+G+++a e+L+sGkalek++ei+ +qGg+  k+e+ie+G++++di +++dGyvt i+nk +t++a+e
  NCBI__GCF_000017185.1:WP_011973334.1 368 GRAQIGQGQKVAWEILESGKALEKFNEIVVEQGGTITKPEEIELGEYTMDIRSPKDGYVTGISNKLITKLAKE 440
                                           ***********************************99************************************ PP

                             TIGR02645 439 aGaPedkgaGvklhvkvgdkvkkGdplytiyaeseekldkaialaralepikveg 493
                                           aG P+dk+aG+ l vk g+kv+k d lytiy++see+ld a++ ar+++pikveg
  NCBI__GCF_000017185.1:WP_011973334.1 441 AGCPKDKKAGIFLGVKTGNKVNKEDILYTIYSSSEERLDAAVNFARRTYPIKVEG 495
                                           *****************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (504 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 19.74
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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