Aligments for a candidate for iolC in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for iolC in Burkholderia phytofirmans PsJN

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate BPHYT_RS13910 BPHYT_RS13910 5-dehydro-2-deoxygluconokinase

Query= reanno::BFirm:BPHYT_RS13910
         (681 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS13910 BPHYT_RS13910
           5-dehydro-2-deoxygluconokinase
          Length = 681

 Score = 1360 bits (3519), Expect = 0.0
 Identities = 681/681 (100%), Positives = 681/681 (100%)

Query: 1   MDQSITSSGVTSASAPATGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKYLG 60
           MDQSITSSGVTSASAPATGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKYLG
Sbjct: 1   MDQSITSSGVTSASAPATGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKYLG 60

Query: 61  GSSANIAFGCARLGLASSMLARVGNDHMGRFLTETLTKEGCDVSHVRIDQERLTALVLLG 120
           GSSANIAFGCARLGLASSMLARVGNDHMGRFLTETLTKEGCDVSHVRIDQERLTALVLLG
Sbjct: 61  GSSANIAFGCARLGLASSMLARVGNDHMGRFLTETLTKEGCDVSHVRIDQERLTALVLLG 120

Query: 121 LKDRDTFPLIFYRENCADMAVDEADFDEAYIASSKALLITGTHFSTEQVNRTSRRALDYA 180
           LKDRDTFPLIFYRENCADMAVDEADFDEAYIASSKALLITGTHFSTEQVNRTSRRALDYA
Sbjct: 121 LKDRDTFPLIFYRENCADMAVDEADFDEAYIASSKALLITGTHFSTEQVNRTSRRALDYA 180

Query: 181 RRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFRIA 240
           RRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFRIA
Sbjct: 181 RRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFRIA 240

Query: 241 GGKTELVDALAMVRAVTPATLVLKRGPMGCQIIDGAVPASLDDLPIHGGVEVEVLNVLGA 300
           GGKTELVDALAMVRAVTPATLVLKRGPMGCQIIDGAVPASLDDLPIHGGVEVEVLNVLGA
Sbjct: 241 GGKTELVDALAMVRAVTPATLVLKRGPMGCQIIDGAVPASLDDLPIHGGVEVEVLNVLGA 300

Query: 301 GDAFASGFLSGWLRDQPLEACARIANASGALVVSRHGCAPAMPTPAELDYFLREAKADPQ 360
           GDAFASGFLSGWLRDQPLEACARIANASGALVVSRHGCAPAMPTPAELDYFLREAKADPQ
Sbjct: 301 GDAFASGFLSGWLRDQPLEACARIANASGALVVSRHGCAPAMPTPAELDYFLREAKADPQ 360

Query: 361 RMRRPDRDATLARLHRVSPARKQWDEVLGFAFDHRNQFFELAQQTGADDARIARLKGLFV 420
           RMRRPDRDATLARLHRVSPARKQWDEVLGFAFDHRNQFFELAQQTGADDARIARLKGLFV
Sbjct: 361 RMRRPDRDATLARLHRVSPARKQWDEVLGFAFDHRNQFFELAQQTGADDARIARLKGLFV 420

Query: 421 EAVAQTESALGLQNRIGVLIDDRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRSIG 480
           EAVAQTESALGLQNRIGVLIDDRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRSIG
Sbjct: 421 EAVAQTESALGLQNRIGVLIDDRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRSIG 480

Query: 481 TTLIPWPQEHIVKCLVQFHPDEPIEQRLEQEAQLRALYDATQASGHELLLEVIPPKHAHL 540
           TTLIPWPQEHIVKCLVQFHPDEPIEQRLEQEAQLRALYDATQASGHELLLEVIPPKHAHL
Sbjct: 481 TTLIPWPQEHIVKCLVQFHPDEPIEQRLEQEAQLRALYDATQASGHELLLEVIPPKHAHL 540

Query: 541 PQAPDTVYRALKRLYNIGIYPEWWKLEPMDAAQWRNVDALIAERDPYCRGVVLLGLSAAV 600
           PQAPDTVYRALKRLYNIGIYPEWWKLEPMDAAQWRNVDALIAERDPYCRGVVLLGLSAAV
Sbjct: 541 PQAPDTVYRALKRLYNIGIYPEWWKLEPMDAAQWRNVDALIAERDPYCRGVVLLGLSAAV 600

Query: 601 EQLDEGFRAAAQSATCRGFTVGRTIFHEPSHAWLAGEIGDDELIGRVRRTFETLIASWRA 660
           EQLDEGFRAAAQSATCRGFTVGRTIFHEPSHAWLAGEIGDDELIGRVRRTFETLIASWRA
Sbjct: 601 EQLDEGFRAAAQSATCRGFTVGRTIFHEPSHAWLAGEIGDDELIGRVRRTFETLIASWRA 660

Query: 661 TRGASAAQSSAPKPVHQEQAA 681
           TRGASAAQSSAPKPVHQEQAA
Sbjct: 661 TRGASAAQSSAPKPVHQEQAA 681


Lambda     K      H
   0.321    0.136    0.409 

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: 1619
Number of extensions: 39
Number of successful extensions: 1
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: 681
Length of database: 681
Length adjustment: 39
Effective length of query: 642
Effective length of database: 642
Effective search space:   412164
Effective search space used:   412164
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 (21.9 bits)
S2: 54 (25.4 bits)

Align candidate BPHYT_RS13910 BPHYT_RS13910 (5-dehydro-2-deoxygluconokinase)
to HMM TIGR04382 (iolC: 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92))

# 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/TIGR04382.hmm
# target sequence database:        /tmp/gapView.16411.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR04382  [M=309]
Accession:   TIGR04382
Description: myo_inos_iolC_N: 5-dehydro-2-deoxygluconokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.9e-121  389.7   0.0   6.4e-121  389.3   0.0    1.1  1  lcl|FitnessBrowser__BFirm:BPHYT_RS13910  BPHYT_RS13910 5-dehydro-2-deoxyg


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS13910  BPHYT_RS13910 5-dehydro-2-deoxygluconokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  389.3   0.0  6.4e-121  6.4e-121       2     309 .]      28     352 ..      27     352 .. 0.99

  Alignments for each domain:
  == domain 1  score: 389.3 bits;  conditional E-value: 6.4e-121
                                TIGR04382   2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreele 71 
                                               d++++GR++vDlyaqq+ga+ledv+sfakylGGs+aNia+g+arlGl ++++++vg+d++Grf++e+l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS13910  28 RDIVCLGRLAVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGCARLGLASSMLARVGNDHMGRFLTETLT 97 
                                              69******************************************************************** PP

                                TIGR04382  72 regvdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgtalske 141
                                              +eg+d+shv  d+e++t+lvll++kd+d+fpl+fYRen+aD+a++ +d de++ia++kall++gt++s+e
  lcl|FitnessBrowser__BFirm:BPHYT_RS13910  98 KEGCDVSHVRIDQERLTALVLLGLKDRDTFPLIFYRENCADMAVDEADFDEAYIASSKALLITGTHFSTE 167
                                              ********************************************************************** PP

                                TIGR04382 142 psreavlkalelakkagvkvvlDiDYRpvlWk............skeeasaalqlvlkkvdviiGteeEf 199
                                              ++++++ +al++a++++v++vlDiDYRpvlW+            ++e ++a+lq++l+++d++iGteeEf
  lcl|FitnessBrowser__BFirm:BPHYT_RS13910 168 QVNRTSRRALDYARRNQVRTVLDIDYRPVLWGltgkadgetrfvASEGVTAHLQRILPLFDLVIGTEEEF 237
                                              ********************************************************************** PP

                                TIGR04382 200 eiaagekddeaaakallelgaelvvvKrGeeGslvytkd.....eeevevkgfkvevlkvlGaGDaFasg 264
                                              +ia g+++   a++ +++++++++v+KrG+ G+  ++++     ++    +g++vevl+vlGaGDaFasg
  lcl|FitnessBrowser__BFirm:BPHYT_RS13910 238 RIAGGKTELVDALAMVRAVTPATLVLKRGPMGCQIIDGAvpaslDDLPIHGGVEVEVLNVLGAGDAFASG 307
                                              *************************************999999888888899****************** PP

                                TIGR04382 265 llygllegedlekalelanAagaivvsrlscaeamptleeleefl 309
                                              +l+g+l++++le ++++anA+ga+vvsr++ca+ampt +el+ fl
  lcl|FitnessBrowser__BFirm:BPHYT_RS13910 308 FLSGWLRDQPLEACARIANASGALVVSRHGCAPAMPTPAELDYFL 352
                                              ******************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (681 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: 00:00:00.01
# Mc/sec: 18.72
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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, or view the source code.

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