Alignments for a candidate for deoB in Desulfitobacterium hafniense DCB-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Desulfitobacterium hafniense DCB-2

Align phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_005811028.1 DHAF_RS17220 phosphopentomutase

Query= BRENDA::Q9WY14
         (390 letters)



>NCBI__GCF_000021925.1:WP_005811028.1
          Length = 388

 Score =  468 bits (1203), Expect = e-136
 Identities = 236/383 (61%), Positives = 289/383 (75%), Gaps = 2/383 (0%)

Query: 2   RVVLIVLDSVGIGEMPDAHLYGDEGSNTIVNTAKAVSGLHLPNMAKLGLGNLDDIPGVEP 61
           R +LIVLDSVGIGEMPDAH YGD GSNTI N AKA  GLHLP++ +LGLGN+  I GV+P
Sbjct: 3   RAILIVLDSVGIGEMPDAHEYGDVGSNTIGNIAKARGGLHLPHLQRLGLGNIAPIQGVDP 62

Query: 62  VKPAEGIYGKMMEKSPGKDTTTGHWEIAGVILKKPFDLFPEGFPKELIEEFERRTGRKVI 121
               +G YGKM E+SPGKDTTTGHWEIAGV+L++ F  F +GFP++ ++ F  R GR+VI
Sbjct: 63  EASPQGCYGKMAERSPGKDTTTGHWEIAGVVLERAFPTFSKGFPEDFLQAFAERIGRQVI 122

Query: 122 GNKPASGTEIIKELGPIHEKTGALIVYTSADSVFQIAAKKEIVPLEELYRYCEIARELLN 181
           GN+ ASGTEII+ LG  H +TG  I YTSADSVFQIAA +E++PLEELYR C IARE+L 
Sbjct: 123 GNEVASGTEIIQRLGQEHVRTGKPIAYTSADSVFQIAAHEEVIPLEELYRICGIAREML- 181

Query: 182 EMGYKVARVIARPFTGEWPNYVRTPERKDFSLEPEGKTLLDVLTENGIPVYGVGKIADIF 241
           E   +V RVIARPF GE  N+ RT  R D+++EP  K LLD++ E G+ V  VGKI DI+
Sbjct: 182 EGDLRVGRVIARPFLGEEGNFYRTTNRHDYAIEPPHKILLDMVKEKGLRVMAVGKIKDIY 241

Query: 242 AGRGVTENYKTKDNNDGIDKTISLMKEKNHDCLIFTNLVDFDTKYGHRNDPVSYAKALEE 301
           AG GVT++  +K N DG++KT++ ++EK    LI TNLVDFD  YGHRND  +YA+ALEE
Sbjct: 242 AGHGVTDHLASKGNRDGVEKTLAFIREKKPG-LIMTNLVDFDMLYGHRNDVENYAQALEE 300

Query: 302 FDARLPEIMHNLNEDDVLFITADHGCDPTTPSTDHSREMVPLLGYGGRLKKDVYVGIRET 361
           FD RLPEI+ +L E+D+LFITADHGCDPTT STDHSRE VPLL YG ++     +GIR +
Sbjct: 301 FDGRLPEILASLEEEDILFITADHGCDPTTESTDHSREYVPLLVYGKKVVPGRNLGIRSS 360

Query: 362 FADLGQTIADIFGVPPLENGTSF 384
           FADLG TIA+  G   L NG SF
Sbjct: 361 FADLGATIAEYLGTEELVNGRSF 383


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: 550
Number of extensions: 17
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: 390
Length of database: 388
Length adjustment: 30
Effective length of query: 360
Effective length of database: 358
Effective search space:   128880
Effective search space used:   128880
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_005811028.1 DHAF_RS17220 (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.1273257.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.6e-160  518.0   0.0   7.5e-160  517.8   0.0    1.0  1  NCBI__GCF_000021925.1:WP_005811028.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000021925.1:WP_005811028.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  517.8   0.0  7.5e-160  7.5e-160       1     380 [.       3     381 ..       3     382 .. 0.99

  Alignments for each domain:
  == domain 1  score: 517.8 bits;  conditional E-value: 7.5e-160
                             TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdklnlpnleklGlgkieelagvdaveevlayyaklse 73 
                                           r+ livldsvGiGe +da +++d+G++t+g ia+a  +l+lp l++lGlg+i  ++gvd  + + + y+k+ e
  NCBI__GCF_000021925.1:WP_005811028.1   3 RAILIVLDSVGIGEMPDAHEYGDVGSNTIGNIAKARGGLHLPHLQRLGLGNIAPIQGVDPEASPQGCYGKMAE 75 
                                           789********************************************************************** PP

                             TIGR01696  74 assGkdtmtGhweiaGlnilkefkvfsngfpeelldkleeragrkvlgnkpasGtvildelGeehmktGkliv 146
                                            s Gkdt+tGhweiaG+ + + f  fs+gfpe++l+ + er gr+v+gn  asGt i+++lG+eh++tGk+i 
  NCBI__GCF_000021925.1:WP_005811028.1  76 RSPGKDTTTGHWEIAGVVLERAFPTFSKGFPEDFLQAFAERIGRQVIGNEVASGTEIIQRLGQEHVRTGKPIA 148
                                           ************************************************************************* PP

                             TIGR01696 147 ytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGeaGnfkrtsnrhdyalkpfaktv 219
                                           ytsadsv+qiaaheev+pleely++c +are+l +++  +Gr+iarpf+Ge Gnf rt+nrhdya++p+ k +
  NCBI__GCF_000021925.1:WP_005811028.1 149 YTSADSVFQIAAHEEVIPLEELYRICGIAREML-EGDLRVGRVIARPFLGEEGNFYRTTNRHDYAIEPPHKIL 220
                                           ******************************975.799************************************ PP

                             TIGR01696 220 ldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftgisfanlvdfdalyGhrrdkeG 292
                                           ld +k++++ v+++Gki+diy+g G+t++  +k+n dg++k++  ++e+  g+ ++nlvdfd lyGhr d+e 
  NCBI__GCF_000021925.1:WP_005811028.1 221 LDMVKEKGLRVMAVGKIKDIYAGHGVTDHLASKGNRDGVEKTLAFIREKKPGLIMTNLVDFDMLYGHRNDVEN 293
                                           ************************************************************************* PP

                             TIGR01696 293 yaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqalesaetfadiGa 365
                                           ya+aleefd rlpe+l+ l e+d+l +tadhG+dpt++ tdh+rey+p+lvy++kv +g+ l+ + +fad+Ga
  NCBI__GCF_000021925.1:WP_005811028.1 294 YAQALEEFDGRLPEILASLEEEDILFITADHGCDPTTESTDHSREYVPLLVYGKKVVPGRNLGIRSSFADLGA 366
                                           ************************************************************************* PP

                             TIGR01696 366 tladnfntskpeyGk 380
                                           t+a++++t++   G+
  NCBI__GCF_000021925.1:WP_005811028.1 367 TIAEYLGTEELVNGR 381
                                           ********9887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (388 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: 00:00:00.00
# Mc/sec: 25.89
//
[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