Alignments for a candidate for iolC in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_04459 H281DRAFT_04459 5-dehydro-2-deoxygluconokinase

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



>FitnessBrowser__Burk376:H281DRAFT_04459
          Length = 682

 Score = 1258 bits (3254), Expect = 0.0
 Identities = 626/683 (91%), Positives = 651/683 (95%), Gaps = 3/683 (0%)

Query: 1   MDQSITSSGVTSASAP--ATGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKY 58
           M QS T SG T A  P  A GSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKY
Sbjct: 1   MAQSSTFSG-TPAQQPGGAAGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKY 59

Query: 59  LGGSSANIAFGCARLGLASSMLARVGNDHMGRFLTETLTKEGCDVSHVRIDQERLTALVL 118
           LGGSSANIAFGCARLGLAS+MLARVGNDHMGRFLTETLTKEGCDVSHVR+D ERLTALVL
Sbjct: 60  LGGSSANIAFGCARLGLASAMLARVGNDHMGRFLTETLTKEGCDVSHVRVDPERLTALVL 119

Query: 119 LGLKDRDTFPLIFYRENCADMAVDEADFDEAYIASSKALLITGTHFSTEQVNRTSRRALD 178
           LGLKDRDTFPLIFYRENCADMAVDEADFDEA+IASSKALLITGTHFSTEQVNRTSRRALD
Sbjct: 120 LGLKDRDTFPLIFYRENCADMAVDEADFDEAFIASSKALLITGTHFSTEQVNRTSRRALD 179

Query: 179 YARRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFR 238
           YARRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFR
Sbjct: 180 YARRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFR 239

Query: 239 IAGGKTELVDALAMVRAVTPATLVLKRGPMGCQIIDGAVPASLDDLPIHGGVEVEVLNVL 298
           IAGGK++L+DALAMVRAVTPATLVLKRGPMGCQIIDG VPASLDD P+HGGVEVEVLNVL
Sbjct: 240 IAGGKSDLLDALAMVRAVTPATLVLKRGPMGCQIIDGEVPASLDDTPVHGGVEVEVLNVL 299

Query: 299 GAGDAFASGFLSGWLRDQPLEACARIANASGALVVSRHGCAPAMPTPAELDYFLREAKAD 358
           GAGDAFASGFLSGWLRDQPL+ACAR ANASGALVVSRH CAPAMPTPAELDYFLREAKAD
Sbjct: 300 GAGDAFASGFLSGWLRDQPLDACARAANASGALVVSRHACAPAMPTPAELDYFLREAKAD 359

Query: 359 PQRMRRPDRDATLARLHRVSPARKQWDEVLGFAFDHRNQFFELAQQTGADDARIARLKGL 418
           P+RMRRPDRDATLARLHRV+PARKQWDEVLGFAFDHRNQFFELAQQ+GA +ARIA+LKGL
Sbjct: 360 PERMRRPDRDATLARLHRVTPARKQWDEVLGFAFDHRNQFFELAQQSGASEARIAQLKGL 419

Query: 419 FVEAVAQTESALGLQNRIGVLIDDRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRS 478
           FV+AVAQTESALGLQ RIGVLID RYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRS
Sbjct: 420 FVDAVAQTESALGLQGRIGVLIDSRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRS 479

Query: 479 IGTTLIPWPQEHIVKCLVQFHPDEPIEQRLEQEAQLRALYDATQASGHELLLEVIPPKHA 538
           +GTTL+ WPQEH+ KCLVQFHPDEP+EQRLEQEAQLRALYDATQASGHELLLEVIPPKHA
Sbjct: 480 VGTTLVSWPQEHVAKCLVQFHPDEPVEQRLEQEAQLRALYDATQASGHELLLEVIPPKHA 539

Query: 539 HLPQAPDTVYRALKRLYNIGIYPEWWKLEPMDAAQWRNVDALIAERDPYCRGVVLLGLSA 598
           +LPQ PD VYRALKRLYNIGIYPEWWKLEPMDAAQWRN+DALIAERDPYCRGVVLLGLSA
Sbjct: 540 NLPQGPDIVYRALKRLYNIGIYPEWWKLEPMDAAQWRNIDALIAERDPYCRGVVLLGLSA 599

Query: 599 AVEQLDEGFRAAAQSATCRGFTVGRTIFHEPSHAWLAGEIGDDELIGRVRRTFETLIASW 658
            VEQL+EGFRAAA+S+TCRGFTVGRTIFHEPSHAWLAGEIGDDELI RVRRTFETLIASW
Sbjct: 600 GVEQLNEGFRAAARSSTCRGFTVGRTIFHEPSHAWLAGEIGDDELIARVRRTFETLIASW 659

Query: 659 RATRGASAAQSSAPKPVHQEQAA 681
           RA R  +AA+  A   VHQEQAA
Sbjct: 660 RAARDTAAAERGASNRVHQEQAA 682


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: 1527
Number of extensions: 41
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: 682
Length adjustment: 39
Effective length of query: 642
Effective length of database: 643
Effective search space:   412806
Effective search space used:   412806
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 H281DRAFT_04459 H281DRAFT_04459 (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.17965.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   3.5e-122  393.5   0.0   4.7e-122  393.1   0.0    1.2  1  lcl|FitnessBrowser__Burk376:H281DRAFT_04459  H281DRAFT_04459 5-dehydro-2-deox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_04459  H281DRAFT_04459 5-dehydro-2-deoxygluconokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.1   0.0  4.7e-122  4.7e-122       2     309 .]      29     353 ..      28     353 .. 0.99

  Alignments for each domain:
  == domain 1  score: 393.1 bits;  conditional E-value: 4.7e-122
                                    TIGR04382   2 ldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvr 67 
                                                   d++++GR++vDlyaqq+ga+ledv+sfakylGGs+aNia+g+arlGl +a++++vg+d++Grf++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04459  29 RDIVCLGRLAVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGCARLGLASAMLARVGNDHMGRFLT 94 
                                                  69**************************************************************** PP

                                    TIGR04382  68 eeleregvdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallv 133
                                                  e+l++eg+d+shv  d+e++t+lvll++kd+d+fpl+fYRen+aD+a++ +d de++ia++kall+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04459  95 ETLTKEGCDVSHVRVDPERLTALVLLGLKDRDTFPLIFYRENCADMAVDEADFDEAFIASSKALLI 160
                                                  ****************************************************************** PP

                                    TIGR04382 134 sgtalskepsreavlkalelakkagvkvvlDiDYRpvlWk............skeeasaalqlvlk 187
                                                  +gt++s+e++++++ +al++a++++v++vlDiDYRpvlW+            ++e ++a+lq++l+
  lcl|FitnessBrowser__Burk376:H281DRAFT_04459 161 TGTHFSTEQVNRTSRRALDYARRNQVRTVLDIDYRPVLWGltgkadgetrfvASEGVTAHLQRILP 226
                                                  ****************************************************************** PP

                                    TIGR04382 188 kvdviiGteeEfeiaagekddeaaakallelgaelvvvKrGeeGslvytkd.....eeevevkgfk 248
                                                  ++d++iGteeEf+ia g++d   a++ +++++++++v+KrG+ G+  ++++     +++   +g++
  lcl|FitnessBrowser__Burk376:H281DRAFT_04459 227 LFDLVIGTEEEFRIAGGKSDLLDALAMVRAVTPATLVLKRGPMGCQIIDGEvpaslDDTPVHGGVE 292
                                                  **************************************************99***9999999**** PP

                                    TIGR04382 249 vevlkvlGaGDaFasgllygllegedlekalelanAagaivvsrlscaeamptleeleefl 309
                                                  vevl+vlGaGDaFasg+l+g+l++++l+ +++ anA+ga+vvsr++ca+ampt +el+ fl
  lcl|FitnessBrowser__Burk376:H281DRAFT_04459 293 VEVLNVLGAGDAFASGFLSGWLRDQPLDACARAANASGALVVSRHACAPAMPTPAELDYFL 353
                                                  **********************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (682 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: 21.24
//
[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
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