Alignments for a candidate for deoB in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoB in Rhodobacter johrii JA192

Align Phosphopentomutase (EC 5.4.2.7) (characterized)
to candidate WP_069330267.1 C8J29_RS21715 phosphopentomutase

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



>NCBI__GCF_003046325.1:WP_069330267.1
          Length = 398

 Score =  574 bits (1479), Expect = e-168
 Identities = 288/398 (72%), Positives = 318/398 (79%), Gaps = 2/398 (0%)

Query: 1   MTRAFLIVMDSVGCGGAPDAADFGDEGANTLAHIAQACAAGRADAGRSGPLRMPVLDGLG 60
           M RAFLIVMDSVGCGGAPDAA FGD G+NTL HIA+ACAAGRA+ GRSGPLR+PVLD LG
Sbjct: 1   MPRAFLIVMDSVGCGGAPDAAAFGDAGSNTLGHIAEACAAGRAEEGRSGPLRLPVLDALG 60

Query: 61  LGAAIRLASGAETPGLAATPTGLWGAATEVSRGKDTPTGHWELAGVPVPWEWTTFPDTDP 120
           LG AI L SG   PGL A P+G WGAATEVS+GKDTP+GHWELAGVPVPW+W  FPD  P
Sbjct: 61  LGRAIELGSGLRPPGLGAEPSGRWGAATEVSKGKDTPSGHWELAGVPVPWDWHYFPDRCP 120

Query: 121 AFPPDLLAEMARAAGTEGTLCNTHASGTEVIERFGAEHLRTGWPICYTSVDSVLQIAAHE 180
           AFP DL AE+ R AGTEG L N HASGT VIE  GAEHLRTGWPICYTS DSVLQIAAHE
Sbjct: 121 AFPDDLTAEICRRAGTEGILGNRHASGTAVIEELGAEHLRTGWPICYTSADSVLQIAAHE 180

Query: 181 EAFGLDRLLDVCETLAPRLHAMKVGRVIARPFLGSEATGFARTQNRRDFAIAPPAPTLCD 240
           EAFGLDRLL +C  LAP LHAM+VGRVIARPF G+  + FART NRRD+AIAPPAPTL D
Sbjct: 181 EAFGLDRLLALCAGLAPTLHAMRVGRVIARPFTGAPGS-FARTPNRRDYAIAPPAPTLLD 239

Query: 241 RVQAAGRRVHAIGKIKDIFSGRGIDTVAKG-SDAALMEALIAAGQVAEEGSLTFANFVEF 299
              AAGR  HAIGKI DIFS RGI  + KG  DAAL + L A    AEEG+LTFANFVEF
Sbjct: 240 VAAAAGRATHAIGKIGDIFSHRGIGQLHKGRDDAALFDRLDALAGAAEEGALTFANFVEF 299

Query: 300 DSLYGHRRDVAGYARALEWFDAQLPRFLATLRPGDLAIFTADHGNDPTWHGTEHTRERVP 359
           DSLYGHRRDV+GYARALEWFDA+   FLA LRPGD+A+FTADHGNDPT+ GTEHTRERVP
Sbjct: 300 DSLYGHRRDVSGYARALEWFDARAGAFLARLRPGDMALFTADHGNDPTFRGTEHTRERVP 359

Query: 360 VVGYGVGVHEVGIVGFRDVGATIGAHLGVEMFDMGKAM 397
           V+  G G   +G+  + DV AT+ AHLG+     G+A+
Sbjct: 360 VLIAGTGAGPLGLCAYADVAATVAAHLGLLNPGPGRAL 397


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: 639
Number of extensions: 29
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: 398
Length adjustment: 31
Effective length of query: 368
Effective length of database: 367
Effective search space:   135056
Effective search space used:   135056
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 WP_069330267.1 C8J29_RS21715 (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.2039929.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-121  392.1   0.0   1.4e-121  391.9   0.0    1.0  1  NCBI__GCF_003046325.1:WP_069330267.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003046325.1:WP_069330267.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  391.9   0.0  1.4e-121  1.4e-121       1     374 [.       3     389 ..       3     396 .. 0.93

  Alignments for each domain:
  == domain 1  score: 391.9 bits;  conditional E-value: 1.4e-121
                             TIGR01696   1 rvflivldsvGiGeaedaadfkdeGadtlghiaealdk..........lnlpnleklGlgkiee....lagvd 59 
                                           r+fliv+dsvG G a+daa f+d G++tlghiaea++           l+lp l+ lGlg++ e    l+   
  NCBI__GCF_003046325.1:WP_069330267.1   3 RAFLIVMDSVGCGGAPDAAAFGDAGSNTLGHIAEACAAgraeegrsgpLRLPVLDALGLGRAIElgsgLRPPG 75 
                                           89***********************************99**********************999666633334 PP

                             TIGR01696  60 aveevlayyaklseassGkdtmtGhweiaGlnilkefkvfs...ngfpeelldkleeragrk.vlgnkpasGt 128
                                             +e+ + ++ + e+s+Gkdt++Ghwe+aG+++  ++++f+    +fp++l  ++ +rag + +lgn++asGt
  NCBI__GCF_003046325.1:WP_069330267.1  76 LGAEPSGRWGAATEVSKGKDTPSGHWELAGVPVPWDWHYFPdrcPAFPDDLTAEICRRAGTEgILGNRHASGT 148
                                           5689*************************************77679***************99********** PP

                             TIGR01696 129 vildelGeehmktGklivytsadsvlqiaaheevvpleelyelcekarellkdpkyliGriiarpfvGeaGnf 201
                                           ++++elG eh++tG +i ytsadsvlqiaahee ++l++l  lc      l+     +Gr+iarpf G +G f
  NCBI__GCF_003046325.1:WP_069330267.1 149 AVIEELGAEHLRTGWPICYTSADSVLQIAAHEEAFGLDRLLALCAGLAPTLH--AMRVGRVIARPFTGAPGSF 219
                                           ********************************************98877665..578**************** PP

                             TIGR01696 202 krtsnrhdyalkpfaktvldklkdekydvisiGkiadiydgeGitkkvrtksnmdgldkvikelkedftg.is 273
                                            rt+nr dya+ p+a+t+ld    ++    +iGki di++  Gi +  + +   +++d++    + + +g ++
  NCBI__GCF_003046325.1:WP_069330267.1 220 ARTPNRRDYAIAPPAPTLLDVAAAAGRATHAIGKIGDIFSHRGIGQLHKGRDDAALFDRLDALAGAAEEGaLT 292
                                           ***********************************************************988888888889** PP

                             TIGR01696 274 fanlvdfdalyGhrrdkeGyaaaleefdarlpellsklreddlliltadhGndptatGtdhtreyipvlvysp 346
                                           fan+v+fd+lyGhrrd++Gya+ale fdar   +l++lr  d+ ++tadhGndpt++Gt+htre +pvl+ + 
  NCBI__GCF_003046325.1:WP_069330267.1 293 FANFVEFDSLYGHRRDVSGYARALEWFDARAGAFLARLRPGDMALFTADHGNDPTFRGTEHTRERVPVLIAGT 365
                                           **********************************************************************997 PP

                             TIGR01696 347 kvkkgqalesaetfadiGatladnfnts 374
                                              +   l++  ++ad+ at+a +++  
  NCBI__GCF_003046325.1:WP_069330267.1 366 GAGP---LGL-CAYADVAATVAAHLGLL 389
                                           6544...444.46888999988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (381 nodes)
Target sequences:                          1  (398 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: 29.46
//
[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 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