Alignments for a candidate for iolC in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Pseudomonas fluorescens FW300-N2C3

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 AO356_23160 AO356_23160 5-dehydro-2-deoxygluconokinase

Query= reanno::pseudo5_N2C3_1:AO356_23160
         (645 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23160
          Length = 645

 Score = 1284 bits (3323), Expect = 0.0
 Identities = 645/645 (100%), Positives = 645/645 (100%)

Query: 1   MGQTRFASGRQLDVICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR 60
           MGQTRFASGRQLDVICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR
Sbjct: 1   MGQTRFASGRQLDVICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR 60

Query: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENC 120
           SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENC
Sbjct: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENC 120

Query: 121 ADMALRAEDIDETFIASSKALLITGTHFSTDGVYKASIQALDYAQKHQVKRVLDIDYRPV 180
           ADMALRAEDIDETFIASSKALLITGTHFSTDGVYKASIQALDYAQKHQVKRVLDIDYRPV
Sbjct: 121 ADMALRAEDIDETFIASSKALLITGTHFSTDGVYKASIQALDYAQKHQVKRVLDIDYRPV 180

Query: 181 LWGLASKADGETRFVADQKVSQHVQSILPRFDLIVGTEEEFLIAGGSEDLLTALRTVRSL 240
           LWGLASKADGETRFVADQKVSQHVQSILPRFDLIVGTEEEFLIAGGSEDLLTALRTVRSL
Sbjct: 181 LWGLASKADGETRFVADQKVSQHVQSILPRFDLIVGTEEEFLIAGGSEDLLTALRTVRSL 240

Query: 241 TAATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLAGWLEDA 300
           TAATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLAGWLEDA
Sbjct: 241 TAATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLAGWLEDA 300

Query: 301 SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFDSPVPITRPDQDVVLQRLHQVSVP 360
           SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFDSPVPITRPDQDVVLQRLHQVSVP
Sbjct: 301 SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFDSPVPITRPDQDVVLQRLHQVSVP 360

Query: 361 RKTWKQLFIFAFDHRGQLVELAQKGGRELSSIGELKQLFIQAVARVEADLRHQGIEADVG 420
           RKTWKQLFIFAFDHRGQLVELAQKGGRELSSIGELKQLFIQAVARVEADLRHQGIEADVG
Sbjct: 361 RKTWKQLFIFAFDHRGQLVELAQKGGRELSSIGELKQLFIQAVARVEADLRHQGIEADVG 420

Query: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480
           LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ
Sbjct: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480

Query: 481 FHPDDEPLLRLEQEAQLMGLYKASEASGHELLLEVIPPKDHPSPHPDVLYRALKRLYNLG 540
           FHPDDEPLLRLEQEAQLMGLYKASEASGHELLLEVIPPKDHPSPHPDVLYRALKRLYNLG
Sbjct: 481 FHPDDEPLLRLEQEAQLMGLYKASEASGHELLLEVIPPKDHPSPHPDVLYRALKRLYNLG 540

Query: 541 IFPAWWKIEAQGADEWQQLDELIQQRDPYCRGVVLLGLNAPAAALAEGFRQASQSSTCRG 600
           IFPAWWKIEAQGADEWQQLDELIQQRDPYCRGVVLLGLNAPAAALAEGFRQASQSSTCRG
Sbjct: 541 IFPAWWKIEAQGADEWQQLDELIQQRDPYCRGVVLLGLNAPAAALAEGFRQASQSSTCRG 600

Query: 601 FAVGRTIFQEPSRAWLAGEIDDETLIQQVQGRFVELIEAWRAARS 645
           FAVGRTIFQEPSRAWLAGEIDDETLIQQVQGRFVELIEAWRAARS
Sbjct: 601 FAVGRTIFQEPSRAWLAGEIDDETLIQQVQGRFVELIEAWRAARS 645


Lambda     K      H
   0.322    0.137    0.413 

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: 1464
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: 645
Length of database: 645
Length adjustment: 38
Effective length of query: 607
Effective length of database: 607
Effective search space:   368449
Effective search space used:   368449
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 AO356_23160 AO356_23160 (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.20379.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   7.5e-126  405.5   0.0   9.7e-126  405.2   0.0    1.1  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23160  AO356_23160 5-dehydro-2-deoxyglu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23160  AO356_23160 5-dehydro-2-deoxygluconokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.2   0.0  9.7e-126  9.7e-126       1     308 [.      11     335 ..      11     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 405.2 bits;  conditional E-value: 9.7e-126
                                       TIGR04382   1 kldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlG 63 
                                                     +ld+i++GR+gvDlyaqq+ga+ledv+sfakylGGs+aNia+g+arlGl++a++++vgdd++G
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23160  11 QLDVICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLRSAMLSRVGDDHMG 73 
                                                     68************************************************************* PP

                                       TIGR04382  64 rfvreeleregvdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeelia 126
                                                     rf+ e+l+reg+d+s+++ d+e++t++vll+ikd+++fpl+fYRen+aD+al+++d+de++ia
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23160  74 RFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENCADMALRAEDIDETFIA 136
                                                     *************************************************************** PP

                                       TIGR04382 127 eakallvsgtalskepsreavlkalelakkagvkvvlDiDYRpvlWk............skee 177
                                                     ++kall++gt++s++ + +a+++al++a+k++vk vlDiDYRpvlW+            ++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23160 137 SSKALLITGTHFSTDGVYKASIQALDYAQKHQVKRVLDIDYRPVLWGlaskadgetrfvADQK 199
                                                     *************************************************************** PP

                                       TIGR04382 178 asaalqlvlkkvdviiGteeEfeiaagekddeaaakallelgaelvvvKrGeeGslvytkd.. 238
                                                     +s+++q++l+++d+i+GteeEf ia g++d  +a++++++l+a+++vvK G++G++v++++  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23160 200 VSQHVQSILPRFDLIVGTEEEFLIAGGSEDLLTALRTVRSLTAATLVVKLGPQGCTVIHGAip 262
                                                     *************************************************************** PP

                                       TIGR04382 239 ...eeevevkgfkvevlkvlGaGDaFasgllygllegedlekalelanAagaivvsrlscaea 298
                                                        e+   ++g++vevl+vlGaGDaF+sg+l g+le+ + e++++lanA+g +vvsr++ca+a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23160 263 arlEDGAIYPGVRVEVLNVLGAGDAFMSGFLAGWLEDASDERCCQLANACGGLVVSRHACAPA 325
                                                     **9999********************************************************* PP

                                       TIGR04382 299 mptleeleef 308
                                                     mpt +el+ +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_23160 326 MPTRAELDYL 335
                                                     ******9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (309 nodes)
Target sequences:                          1  (645 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: 15.44
//
[ok]

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

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Candidates (tab-delimited)
Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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