Alignments for a candidate for deoB in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Halomonas desiderata SP1

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_086510572.1 BZY95_RS14225 phosphopentomutase

Query= reanno::MR1:200397
         (404 letters)



>NCBI__GCF_002151265.1:WP_086510572.1
          Length = 412

 Score =  541 bits (1394), Expect = e-158
 Identities = 265/405 (65%), Positives = 314/405 (77%), Gaps = 1/405 (0%)

Query: 1   MKRTVIMMLDSFGVGAAGDAAKFGDVGSDTFGHIAKACAEGKAD-TGRKGPLALPNLARL 59
           M R ++++LDSFG+GAA DA +FGD G+DT GHIA AC+ G+ D   R+G LALPNL RL
Sbjct: 1   MTRAIVLVLDSFGIGAAPDAERFGDAGADTLGHIAAACSRGECDGADRQGSLALPNLGRL 60

Query: 60  GLAHAAMESTGAFAPGFADNVDLIGAYGHAQELSSGKDTPSGHWEMAGVPVLFEWGYFSE 119
           GL HA  ESTGA+A G     ++IGAYGHA E+SSGKDTPSGHWE+AGVPV F+WGYF +
Sbjct: 61  GLFHAHRESTGAWAEGVELPAEVIGAYGHAGEISSGKDTPSGHWEIAGVPVRFDWGYFLD 120

Query: 120 HQNSFPKELTDKILARAGLDGFLGNCHASGTTILEELGEEHMRSGKPIFYTSADSVFQIA 179
            + SFP EL   ++    L G LGNCHASGT I+  LGE+HM SGKPI YTSADSV QIA
Sbjct: 121 REESFPPELLAALIREGELPGVLGNCHASGTEIIARLGEQHMASGKPIVYTSADSVLQIA 180

Query: 180 CHEGTFGLENLYRLCEIAREELEPYNIGRVIARPFDGTGPSDFARTGNRKDYSLEPPAKT 239
            HE +FGL  L+ LCE AR  LEPYNIGRVIARPF G    DF+RT NR+DYS+EPPA T
Sbjct: 181 AHEESFGLARLHALCETARRLLEPYNIGRVIARPFVGQHADDFSRTANRRDYSVEPPAPT 240

Query: 240 VLDKLKAAGGEVVSVGKIADIYAYCGITKKVKANGLEALFDATLAEVKSAGENTIVFTNF 299
           VL KL   GGEV+++GKIADIYA+CG+T+ +KA+G +AL DATLA +  AGE ++V TNF
Sbjct: 241 VLQKLCDDGGEVIAIGKIADIYAHCGVTRTLKASGHDALMDATLAALDEAGERSLVMTNF 300

Query: 300 VDFDSHYGHRRDVAGYAKGLEYFDARLPEMLALLDEDDLLILTADHGCDPTWQGTDHTRE 359
           VDFD+ YGHRRDV GYA  LE FDARLPE+LA L + DLL++TADHGCDPTW GTDHTRE
Sbjct: 301 VDFDTLYGHRRDVTGYAAALEAFDARLPELLARLRDGDLLVITADHGCDPTWHGTDHTRE 360

Query: 360 YVPVLAYGAGLKAGSLGRRNSFADIGQSIASYFKLEPMEYGESFI 404
            VPVLA GAGL  GSLG R++FADIGQS+A++  L PM  G SFI
Sbjct: 361 RVPVLALGAGLAPGSLGARDTFADIGQSLAAHLGLPPMADGTSFI 405


Lambda     K      H
   0.318    0.137    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: 619
Number of extensions: 25
Number of successful extensions: 2
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: 404
Length of database: 412
Length adjustment: 31
Effective length of query: 373
Effective length of database: 381
Effective search space:   142113
Effective search space used:   142113
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate WP_086510572.1 BZY95_RS14225 (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.24669.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     3e-159  515.8   0.0   3.4e-159  515.7   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510572.1  BZY95_RS14225 phosphopentomutase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510572.1  BZY95_RS14225 phosphopentomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  515.7   0.0  3.4e-159  3.4e-159       1     373 [.       3     395 ..       3     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: 515.7 bits;  conditional E-value: 3.4e-159
                                 TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk...........lnlpnleklGlgkiee.... 54 
                                               r+ ++vlds+GiG+a+da++f+d Gadtlghia a+++           l lpnl +lGl +++     
  lcl|NCBI__GCF_002151265.1:WP_086510572.1   3 RAIVLVLDSFGIGAAPDAERFGDAGADTLGHIAAACSRgecdgadrqgsLALPNLGRLGLFHAHRestg 71 
                                               7899*********************************99************************999999 PP

                                 TIGR01696  55 ..lagvdaveevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk 118
                                                  +gv+  +ev+++y+++ e+ssGkdt++GhweiaG+++ +++++f    ++fp ell  l +  +++
  lcl|NCBI__GCF_002151265.1:WP_086510572.1  72 awAEGVELPAEVIGAYGHAGEISSGKDTPSGHWEIAGVPVRFDWGYFLdreESFPPELLAALIREGELP 140
                                               9999*******************************************88889***************** PP

                                 TIGR01696 119 .vlgnkpasGtvildelGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyli 186
                                                vlgn++asGt i+ +lGe+hm +Gk+ivytsadsvlqiaahee ++l +l+ lce+ar ll    y+i
  lcl|NCBI__GCF_002151265.1:WP_086510572.1 141 gVLGNCHASGTEIIARLGEQHMASGKPIVYTSADSVLQIAAHEESFGLARLHALCETARRLLE--PYNI 207
                                               9**********************************************************9985..5*** PP

                                 TIGR01696 187 GriiarpfvGe.aGnfkrtsnrhdyalkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksn 254
                                               Gr+iarpfvG+ a +f rt+nr dy+++p+a+tvl+kl d + +vi+iGkiadiy+ +G+t++ ++ + 
  lcl|NCBI__GCF_002151265.1:WP_086510572.1 208 GRVIARPFVGQhADDFSRTANRRDYSVEPPAPTVLQKLCDDGGEVIAIGKIADIYAHCGVTRTLKASGH 276
                                               **********9999******************************************************* PP

                                 TIGR01696 255 mdgldkvikelkedftg.isfanlvdfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltad 322
                                               ++++d+++  l+e+++  ++++n+vdfd+lyGhrrd++Gyaaale fdarlpell++lr+ dll++tad
  lcl|NCBI__GCF_002151265.1:WP_086510572.1 277 DALMDATLAALDEAGERsLVMTNFVDFDTLYGHRRDVTGYAAALEAFDARLPELLARLRDGDLLVITAD 345
                                               ***************988*************************************************** PP

                                 TIGR01696 323 hGndptatGtdhtreyipvlvyspkvkkgqalesaetfadiGatladnfnt 373
                                               hG+dpt++Gtdhtre +pvl+ +    +g +l+ ++tfadiG++la +++ 
  lcl|NCBI__GCF_002151265.1:WP_086510572.1 346 HGCDPTWHGTDHTRERVPVLALGAGLAPG-SLGARDTFADIGQSLAAHLGL 395
                                               *****************************.****************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (412 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: 8.14
//
[ok]

This GapMind analysis is from Sep 24 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