Alignments for a candidate for iolC in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_512 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain

Query= reanno::pseudo6_N2E2:Pf6N2E2_512
         (645 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512
          Length = 645

 Score = 1290 bits (3338), Expect = 0.0
 Identities = 645/645 (100%), Positives = 645/645 (100%)

Query: 1   MGQTRFASGRQLDVICLGRLGVDLYAQQVGARLEDVASFAKYLGGSSANIAFGTARLGLR 60
           MGQTRFASGRQLDVICLGRLGVDLYAQQVGARLEDVASFAKYLGGSSANIAFGTARLGLR
Sbjct: 1   MGQTRFASGRQLDVICLGRLGVDLYAQQVGARLEDVASFAKYLGGSSANIAFGTARLGLR 60

Query: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENC 120
           SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENC
Sbjct: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENC 120

Query: 121 ADMALRVEDIDETFIASSKALLITGTHFSTDGVYKASTQALDYAEKHNVKCVLDIDYRPV 180
           ADMALRVEDIDETFIASSKALLITGTHFSTDGVYKASTQALDYAEKHNVKCVLDIDYRPV
Sbjct: 121 ADMALRVEDIDETFIASSKALLITGTHFSTDGVYKASTQALDYAEKHNVKCVLDIDYRPV 180

Query: 181 LWGLAGKADGETRFVADQKVSQHVQGILPRFDLIVGTEEEFLIAGGSEDLLSALRTVRSL 240
           LWGLAGKADGETRFVADQKVSQHVQGILPRFDLIVGTEEEFLIAGGSEDLLSALRTVRSL
Sbjct: 181 LWGLAGKADGETRFVADQKVSQHVQGILPRFDLIVGTEEEFLIAGGSEDLLSALRTVRSL 240

Query: 241 TAATLVVKLGAQGCTVIHGAIPARLEDGALYPGVRVEVLNVLGAGDAFMSGFLAGWLEDA 300
           TAATLVVKLGAQGCTVIHGAIPARLEDGALYPGVRVEVLNVLGAGDAFMSGFLAGWLEDA
Sbjct: 241 TAATLVVKLGAQGCTVIHGAIPARLEDGALYPGVRVEVLNVLGAGDAFMSGFLAGWLEDA 300

Query: 301 SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFKSPVPITRPDQDAVLQRLHQVSVP 360
           SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFKSPVPITRPDQDAVLQRLHQVSVP
Sbjct: 301 SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFKSPVPITRPDQDAVLQRLHQVSVP 360

Query: 361 RKTWKQLFIFAFDHRWQLVELAQKGGRDLNCIGDLKQLFIQAVERVEADLQRQGIEADVG 420
           RKTWKQLFIFAFDHRWQLVELAQKGGRDLNCIGDLKQLFIQAVERVEADLQRQGIEADVG
Sbjct: 361 RKTWKQLFIFAFDHRWQLVELAQKGGRDLNCIGDLKQLFIQAVERVEADLQRQGIEADVG 420

Query: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQNSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480
           LLADQRFGQDSLNAATGRGWWVARPVEVQNSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ
Sbjct: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQNSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480

Query: 481 FHPDDEPLLRLEQEAQLMGLYKASQVSGHELLLEVIPPKDHPSPHPDVLYRALKRLYNLG 540
           FHPDDEPLLRLEQEAQLMGLYKASQVSGHELLLEVIPPKDHPSPHPDVLYRALKRLYNLG
Sbjct: 481 FHPDDEPLLRLEQEAQLMGLYKASQVSGHELLLEVIPPKDHPSPHPDVLYRALKRLYNLG 540

Query: 541 IFPAWWKIEAQSAQEWKQLDELIQQRDPYCRGVVLLGLNAPAAALAEGFRQASQSTTCRG 600
           IFPAWWKIEAQSAQEWKQLDELIQQRDPYCRGVVLLGLNAPAAALAEGFRQASQSTTCRG
Sbjct: 541 IFPAWWKIEAQSAQEWKQLDELIQQRDPYCRGVVLLGLNAPAAALAEGFRQASQSTTCRG 600

Query: 601 FAVGRTIFQEPSRAWLAGEIDDETLIRQVQGRFVELIEAWRSARA 645
           FAVGRTIFQEPSRAWLAGEIDDETLIRQVQGRFVELIEAWRSARA
Sbjct: 601 FAVGRTIFQEPSRAWLAGEIDDETLIRQVQGRFVELIEAWRSARA 645


Lambda     K      H
   0.322    0.138    0.417 

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: 1489
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: 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 Pf6N2E2_512 (5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain)
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.7005.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.7e-125  404.4   0.0   2.1e-125  404.0   0.0    1.1  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512  5-keto-2-deoxygluconokinase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512  5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.0   0.0  2.1e-125  2.1e-125       1     308 [.      11     335 ..      11     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 404.0 bits;  conditional E-value: 2.1e-125
                                     TIGR04382   1 kldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrf 65 
                                                   +ld+i++GR+gvDlyaqq+ga+ledv sfakylGGs+aNia+g+arlGl++a++++vgdd++Grf
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512  11 QLDVICLGRLGVDLYAQQVGARLEDVASFAKYLGGSSANIAFGTARLGLRSAMLSRVGDDHMGRF 75 
                                                   68*************************************************************** PP

                                     TIGR04382  66 vreeleregvdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeaka 130
                                                   + e+l+reg+d+s+++ d+e++t++vll+ikd+++fpl+fYRen+aD+al+v+d+de++ia++ka
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512  76 LVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFPLVFYRENCADMALRVEDIDETFIASSKA 140
                                                   ***************************************************************** PP

                                     TIGR04382 131 llvsgtalskepsreavlkalelakkagvkvvlDiDYRpvlWk............skeeasaalq 183
                                                   ll++gt++s++ + +a+ +al++a k++vk vlDiDYRpvlW+            +++++s+++q
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512 141 LLITGTHFSTDGVYKASTQALDYAEKHNVKCVLDIDYRPVLWGlagkadgetrfvADQKVSQHVQ 205
                                                   ***************************************************************** PP

                                     TIGR04382 184 lvlkkvdviiGteeEfeiaagekddeaaakallelgaelvvvKrGeeGslvytkd.....eeeve 243
                                                    +l+++d+i+GteeEf ia g++d   a++++++l+a+++vvK G++G++v++++     e+   
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512 206 GILPRFDLIVGTEEEFLIAGGSEDLLSALRTVRSLTAATLVVKLGAQGCTVIHGAiparlEDGAL 270
                                                   ***********************************************************99**** PP

                                     TIGR04382 244 vkgfkvevlkvlGaGDaFasgllygllegedlekalelanAagaivvsrlscaeamptleeleef 308
                                                   ++g++vevl+vlGaGDaF+sg+l g+le+ + e++++lanA+g +vvsr++ca+ampt +el+ +
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512 271 YPGVRVEVLNVLGAGDAFMSGFLAGWLEDASDERCCQLANACGGLVVSRHACAPAMPTRAELDYL 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.81
//
[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