Alignments for a candidate for deoB in Desulfuromonas acetexigens DSM 1397

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Desulfuromonas acetexigens DSM 1397

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_240746373.1 BQ4888_RS16585 phosphopentomutase

Query= BRENDA::Q9WY14
         (390 letters)



>NCBI__GCF_900111775.1:WP_240746373.1
          Length = 385

 Score =  389 bits (998), Expect = e-112
 Identities = 197/375 (52%), Positives = 256/375 (68%), Gaps = 4/375 (1%)

Query: 3   VVLIVLDSVGIGEMPDAHLYGDEGSNTIVNTAKAVSGLHLPNMAKLGLGNLDDIPGVEPV 62
           ++LI LD  GIGE+PDA  YGD G+NT+ + A+A  GL LP++  LGLGN+  +PGV  V
Sbjct: 1   MLLITLDGCGIGELPDAARYGDVGANTLGHVAEACGGLDLPHLQALGLGNILQLPGVPTV 60

Query: 63  KPAEGIYGKMMEKSPGKDTTTGHWEIAGVILKKPFDLFPEGFPKELIEEFERRTGRKVIG 122
              +G +G+M E S GKDTTTGHWEIAG+I   P   +P GFP+E+I    R TG   +G
Sbjct: 61  AAPQGGWGRMAEASAGKDTTTGHWEIAGIIEPNPLPTYPTGFPEEIIAALRRETGLDFLG 120

Query: 123 NKPASGTEIIKELGPIHEKTGALIVYTSADSVFQIAAKKEIVPLEELYRYCEIARELLNE 182
           N  ASGTEI+KELG  H ++G  IVYTSADSVFQ+AA + I+P+E LY  C  AR +L+ 
Sbjct: 121 NIAASGTEILKELGDEHLRSGRPIVYTSADSVFQVAAHEGIIPVERLYEICRAARRILDP 180

Query: 183 MGYKVARVIARPFTGEWP-NYVRTPERKDFSLEPEGKTLLDVLTENGIPVYGVGKIADIF 241
             Y++ RVIARPF G+ P NY RT  R DFSL P   T+LD +T  GIPV+GVGKI DIF
Sbjct: 181 --YRIGRVIARPFVGDAPENYRRTANRHDFSLSPTAPTILDGMTAAGIPVFGVGKIRDIF 238

Query: 242 AGRGVTENYKTKDNNDGIDKTISLMKEKNHDCLIFTNLVDFDTKYGHRNDPVSYAKALEE 301
           AG G+ +   + DN DG+ KT++ +       LIFTNLVDFD  YGHR D   + +ALEE
Sbjct: 239 AGCGIGDYVYSSDNRDGMAKTLTALAAMERG-LIFTNLVDFDMLYGHRLDAKGFGQALEE 297

Query: 302 FDARLPEIMHNLNEDDVLFITADHGCDPTTPSTDHSREMVPLLGYGGRLKKDVYVGIRET 361
           FD  LPE    L  +D+L +TADHGCDPTTP +DH+RE VPLL +   + +   +G+R +
Sbjct: 298 FDRWLPECRAALKAEDLLIVTADHGCDPTTPGSDHTREYVPLLVWSPAMAQGTALGVRTS 357

Query: 362 FADLGQTIADIFGVP 376
           FAD+  T+A+ +G+P
Sbjct: 358 FADVAATLAEAYGLP 372


Lambda     K      H
   0.317    0.139    0.412 

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: 504
Number of extensions: 25
Number of successful extensions: 4
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: 390
Length of database: 385
Length adjustment: 30
Effective length of query: 360
Effective length of database: 355
Effective search space:   127800
Effective search space used:   127800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_240746373.1 BQ4888_RS16585 (phosphopentomutase)
to HMM TIGR01696 (deoB: phosphopentomutase (EC 5.4.2.7))

# 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/TIGR01696.hmm
# target sequence database:        /tmp/gapView.2071175.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01696  [M=381]
Accession:   TIGR01696
Description: deoB: phosphopentomutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-143  463.9   0.0   2.2e-143  463.7   0.0    1.0  1  NCBI__GCF_900111775.1:WP_240746373.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900111775.1:WP_240746373.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  463.7   0.0  2.2e-143  2.2e-143       4     372 ..       3     370 ..       1     375 [. 0.98

  Alignments for each domain:
  == domain 1  score: 463.7 bits;  conditional E-value: 2.2e-143
                             TIGR01696   4 livldsvGiGeaedaadfkdeGadtlghiaealdklnlpnleklGlgkieelagvdaveevlayyaklseass 76 
                                           li ld  GiGe +daa+++d+Ga+tlgh+aea+ +l+lp l+ lGlg+i +l+gv +v+ + + ++++ eas+
  NCBI__GCF_900111775.1:WP_240746373.1   3 LITLDGCGIGELPDAARYGDVGANTLGHVAEACGGLDLPHLQALGLGNILQLPGVPTVAAPQGGWGRMAEASA 75 
                                           899********************************************************************** PP

                             TIGR01696  77 GkdtmtGhweiaGlnilkefkvfsngfpeelldkleeragrkvlgnkpasGtvildelGeehmktGklivyts 149
                                           Gkdt+tGhweiaG+   ++   ++ gfpee++  l + +g+ +lgn  asGt il elG+eh+++G++ivyts
  NCBI__GCF_900111775.1:WP_240746373.1  76 GKDTTTGHWEIAGIIEPNPLPTYPTGFPEEIIAALRRETGLDFLGNIAASGTEILKELGDEHLRSGRPIVYTS 148
                                           ************************************************************************* PP

                             TIGR01696 150 adsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkrtsnrhdyalkpfaktvld 221
                                           adsv+q+aahe ++p+e+lye+c  ar  l dp y iGr+iarpfvG+ + n++rt+nrhd++l p a+t+ld
  NCBI__GCF_900111775.1:WP_240746373.1 149 ADSVFQVAAHEGIIPVERLYEICRAARRIL-DP-YRIGRVIARPFVGDaPENYRRTANRHDFSLSPTAPTILD 219
                                           ***************************876.55.**************999********************** PP

                             TIGR01696 222 klkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftgisfanlvdfdalyGhrrdkeGya 294
                                            +  ++  v  +Gki di++g+Gi + v +  n dg+ k++  l     g+ f+nlvdfd lyGhr d +G++
  NCBI__GCF_900111775.1:WP_240746373.1 220 GMTAAGIPVFGVGKIRDIFAGCGIGDYVYSSDNRDGMAKTLTALAAMERGLIFTNLVDFDMLYGHRLDAKGFG 292
                                           ************************************************************************* PP

                             TIGR01696 295 aaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadiGatl 367
                                           +aleefd+ lpe  + l+ +dlli+tadhG+dpt++G+dhtrey+p+lv+sp + +g al+ +++fad+ atl
  NCBI__GCF_900111775.1:WP_240746373.1 293 QALEEFDRWLPECRAALKAEDLLIVTADHGCDPTTPGSDHTREYVPLLVWSPAMAQGTALGVRTSFADVAATL 365
                                           ************************************************************************* PP

                             TIGR01696 368 adnfn 372
                                           a+ ++
  NCBI__GCF_900111775.1:WP_240746373.1 366 AEAYG 370
                                           *9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (385 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.13
//
[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