Alignments for a candidate for deoB in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Phaeobacter inhibens BS107

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate GFF1180 PGA1_c11950 phosphopentomutase DeoB

Query= reanno::Dino:3607415
         (399 letters)



>FitnessBrowser__Phaeo:GFF1180
          Length = 406

 Score =  517 bits (1331), Expect = e-151
 Identities = 262/404 (64%), Positives = 302/404 (74%), Gaps = 6/404 (1%)

Query: 1   MTRAFLIVMDSVGCGGAPDAA-----DFGDEGANTLAHIAQACAAGRADAGRSGPLRMPV 55
           M RAFL+VMDSVG GGAPDA      D  D GANTLAHIAQACAAG+A+ GRSGPL +P 
Sbjct: 1   MPRAFLVVMDSVGIGGAPDAGAYFNGDLPDLGANTLAHIAQACAAGQAEEGRSGPLHLPN 60

Query: 56  LDGLGLGAAIRLASGAETPGLA-ATPTGLWGAATEVSRGKDTPTGHWELAGVPVPWEWTT 114
           LD LGLGAA+ L S    P L  A  TG WGAA E+SRGKDTP+GHWELAG+PVPW+W  
Sbjct: 61  LDQLGLGAAVALVSAVPCPDLGGAGVTGRWGAAREISRGKDTPSGHWELAGLPVPWDWCY 120

Query: 115 FPDTDPAFPPDLLAEMARAAGTEGTLCNTHASGTEVIERFGAEHLRTGWPICYTSVDSVL 174
           FPD  PAFP  L+A +  AAGTE  L N HASGT +I   GA H+++G PICYTS DSV 
Sbjct: 121 FPDQTPAFPDHLVAHVCAAAGTEAILGNCHASGTAIIAEHGAAHMQSGLPICYTSADSVF 180

Query: 175 QIAAHEEAFGLDRLLDVCETLAPRLHAMKVGRVIARPFLGSEATGFARTQNRRDFAIAPP 234
           QIAAHEE FGL+RLL +CE +AP LH MKVGRVIARPF+G+  TGF RT NRRD+AI PP
Sbjct: 181 QIAAHEETFGLNRLLALCEAVAPYLHQMKVGRVIARPFIGTPQTGFQRTTNRRDYAIMPP 240

Query: 235 APTLCDRVQAAGRRVHAIGKIKDIFSGRGIDTVAKGSDAALMEALIAAGQVAEEGSLTFA 294
           AP L + VQ AG+ VHAIGKI DIFS +GIDT+ KG DA LM+ L  A   AEEGSLTFA
Sbjct: 241 APILTNWVQDAGQLVHAIGKIGDIFSMQGIDTLKKGDDATLMQYLHDAVAGAEEGSLTFA 300

Query: 295 NFVEFDSLYGHRRDVAGYARALEWFDAQLPRFLATLRPGDLAIFTADHGNDPTWHGTEHT 354
           NFVEFDSLYGHRRD++GYA+ALEWFD ++   L  LR GDL I TADHGNDP+W GT+HT
Sbjct: 301 NFVEFDSLYGHRRDISGYAQALEWFDREIGTLLPRLREGDLLILTADHGNDPSWPGTDHT 360

Query: 355 RERVPVVGYGVGVHEVGIVGFRDVGATIGAHLGVEMFDMGKAML 398
           RE+VPV+  G G   +G +GF DV AT+ AHL V +   G+  L
Sbjct: 361 REQVPVLIAGAGAGPLGTIGFVDVAATVAAHLNVPVQGPGRPAL 404


Lambda     K      H
   0.321    0.137    0.429 

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: 576
Number of extensions: 22
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: 399
Length of database: 406
Length adjustment: 31
Effective length of query: 368
Effective length of database: 375
Effective search space:   138000
Effective search space used:   138000
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: 50 (23.9 bits)

Align candidate GFF1180 PGA1_c11950 (phosphopentomutase DeoB)
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.16978.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   8.4e-120  386.0   0.0   9.7e-120  385.8   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1180  PGA1_c11950 phosphopentomutase D


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1180  PGA1_c11950 phosphopentomutase DeoB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.8   0.0  9.7e-120  9.7e-120       1     373 [.       3     394 ..       3     401 .. 0.90

  Alignments for each domain:
  == domain 1  score: 385.8 bits;  conditional E-value: 9.7e-120
                          TIGR01696   1 rvflivldsvGiGeaedaa.....dfkdeGadtlghiaealdk..........lnlpnleklGlgkiee....lag 57 
                                        r+fl+v+dsvGiG a+da      d+ d Ga+tl hia+a++           l+lpnl++lGlg +      ++ 
  lcl|FitnessBrowser__Phaeo:GFF1180   3 RAFLVVMDSVGIGGAPDAGayfngDLPDLGANTLAHIAQACAAgqaeegrsgpLHLPNLDQLGLGAAVAlvsaVPC 78 
                                        89***************962222245699*************99********************998775444333 PP

                          TIGR01696  58 vd.aveevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGt 128
                                         d + + v + ++ ++e+s Gkdt++Ghwe+aGl++  ++ +f+    +fp+ l+ ++   ag + +lgn++asGt
  lcl|FitnessBrowser__Phaeo:GFF1180  79 PDlGGAGVTGRWGAAREISRGKDTPSGHWELAGLPVPWDWCYFPdqtPAFPDHLVAHVCAAAGTEaILGNCHASGT 154
                                        333568899***********************************76668**************998********** PP

                          TIGR01696 129 vildelGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGe.aGnfkr 203
                                        +i+ e G  hm++G +i ytsadsv+qiaahee+++l++l  lce +   l++   ++Gr+iarpf+G     f+r
  lcl|FitnessBrowser__Phaeo:GFF1180 155 AIIAEHGAAHMQSGLPICYTSADSVFQIAAHEETFGLNRLLALCEAVAPYLHQM--KVGRVIARPFIGTpQTGFQR 228
                                        ************************************************999865..69***********5578*** PP

                          TIGR01696 204 tsnrhdyalkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.isfanlv 278
                                        t+nr dya+ p+a+ + + ++d++  v +iGki di++ +Gi   ++      +++ + + +  + +g ++fan+v
  lcl|FitnessBrowser__Phaeo:GFF1180 229 TTNRRDYAIMPPAPILTNWVQDAGQLVHAIGKIGDIFSMQGIDTLKK-GDDATLMQYLHDAVAGAEEGsLTFANFV 303
                                        ******************************************87655.456778999999999999988******* PP

                          TIGR01696 279 dfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvyspkvkkgqal 354
                                        +fd+lyGhrrd +Gya+ale fd+ +  ll +lre dlliltadhGndp ++Gtdhtre +pvl+ +    +    
  lcl|FitnessBrowser__Phaeo:GFF1180 304 EFDSLYGHRRDISGYAQALEWFDREIGTLLPRLREGDLLILTADHGNDPSWPGTDHTREQVPVLIAGAGAGPL--- 376
                                        *****************************************************************99765554... PP

                          TIGR01696 355 esaetfadiGatladnfnt 373
                                        + +  f d+ at+a ++n+
  lcl|FitnessBrowser__Phaeo:GFF1180 377 G-TIGFVDVAATVAAHLNV 394
                                        3.34688888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (406 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: 00:00:00.02
# Mc/sec: 7.10
//
[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