Alignments for a candidate for iolC in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Pseudomonas simiae WCS417

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 GFF2324 PS417_11850 5-dehydro-2-deoxygluconokinase

Query= reanno::WCS417:GFF2324
         (645 letters)



>FitnessBrowser__WCS417:GFF2324
          Length = 645

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

Query: 1   MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR 60
           MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR
Sbjct: 1   MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLR 60

Query: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTALVLLGLKDRETFPLVFYRENC 120
           SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTALVLLGLKDRETFPLVFYRENC
Sbjct: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTALVLLGLKDRETFPLVFYRENC 120

Query: 121 ADMALRAEDISEAFIASSKALLITGTHFSTDGVYKASIQALDYAAKHNVQRVLDIDYRPV 180
           ADMALRAEDISEAFIASSKALLITGTHFSTDGVYKASIQALDYAAKHNVQRVLDIDYRPV
Sbjct: 121 ADMALRAEDISEAFIASSKALLITGTHFSTDGVYKASIQALDYAAKHNVQRVLDIDYRPV 180

Query: 181 LWGLAGKADGETRFVADQNVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLTALRKVREL 240
           LWGLAGKADGETRFVADQNVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLTALRKVREL
Sbjct: 181 LWGLAGKADGETRFVADQNVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLTALRKVREL 240

Query: 241 TQATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWINDA 300
           TQATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWINDA
Sbjct: 241 TQATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWINDA 300

Query: 301 SDERCSQLANACGGLVVSRHACAPAMPTPAELEYLFNSPVPITRPDQDLTLQRLHRVTVP 360
           SDERCSQLANACGGLVVSRHACAPAMPTPAELEYLFNSPVPITRPDQDLTLQRLHRVTVP
Sbjct: 301 SDERCSQLANACGGLVVSRHACAPAMPTPAELEYLFNSPVPITRPDQDLTLQRLHRVTVP 360

Query: 361 RKAWKQLFVFAFDHRWQLVDLAQKGGQDLARISDAKQLFIQAIERVEKKLAEQGVEADVG 420
           RKAWKQLFVFAFDHRWQLVDLAQKGGQDLARISDAKQLFIQAIERVEKKLAEQGVEADVG
Sbjct: 361 RKAWKQLFVFAFDHRWQLVDLAQKGGQDLARISDAKQLFIQAIERVEKKLAEQGVEADVG 420

Query: 421 LLADQRFGQDALNAASGRGWWIARPVEVQNSRPLAFEHGRSVGSNLIAWPQEQIIKCLVQ 480
           LLADQRFGQDALNAASGRGWWIARPVEVQNSRPLAFEHGRSVGSNLIAWPQEQIIKCLVQ
Sbjct: 421 LLADQRFGQDALNAASGRGWWIARPVEVQNSRPLAFEHGRSVGSNLIAWPQEQIIKCLVQ 480

Query: 481 FHPDDEPLLRLEQEAQLKAVYEASIVSGHELLLEVIPPKDHPSTYPDVLYRSLKRLYNLG 540
           FHPDDEPLLRLEQEAQLKAVYEASIVSGHELLLEVIPPKDHPSTYPDVLYRSLKRLYNLG
Sbjct: 481 FHPDDEPLLRLEQEAQLKAVYEASIVSGHELLLEVIPPKDHPSTYPDVLYRSLKRLYNLG 540

Query: 541 IYPAWWKIEAQSAEDWKKLDELIQERDPYCRGVVLLGLNASAEFLADGFQQASQSTTCRG 600
           IYPAWWKIEAQSAEDWKKLDELIQERDPYCRGVVLLGLNASAEFLADGFQQASQSTTCRG
Sbjct: 541 IYPAWWKIEAQSAEDWKKLDELIQERDPYCRGVVLLGLNASAEFLADGFQQASQSTTCRG 600

Query: 601 FAVGRTIFQEPSRAWMAGEIDDEVLIQQVQATFEQLINAWRSARN 645
           FAVGRTIFQEPSRAWMAGEIDDEVLIQQVQATFEQLINAWRSARN
Sbjct: 601 FAVGRTIFQEPSRAWMAGEIDDEVLIQQVQATFEQLINAWRSARN 645


Lambda     K      H
   0.321    0.137    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: 1485
Number of extensions: 31
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 (21.8 bits)
S2: 54 (25.4 bits)

Align candidate GFF2324 PS417_11850 (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.24092.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   2.2e-124  400.7   0.0   2.8e-124  400.3   0.0    1.1  1  lcl|FitnessBrowser__WCS417:GFF2324  PS417_11850 5-dehydro-2-deoxyglu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2324  PS417_11850 5-dehydro-2-deoxygluconokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.3   0.0  2.8e-124  2.8e-124       1     308 [.      11     335 ..      11     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 400.3 bits;  conditional E-value: 2.8e-124
                           TIGR04382   1 kldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGrfvreeleregv 75 
                                         +ldli++GR+gvDlyaqq+ga+ledv+sfakylGGs+aNia+g+arlGl++a++++vgdd++Grf+ e+l+reg+
  lcl|FitnessBrowser__WCS417:GFF2324  11 QLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLRSAMLSRVGDDHMGRFLVESLAREGC 85 
                                         68************************************************************************* PP

                           TIGR04382  76 dtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaeakallvsgtalskepsreavlka 150
                                         d+s+++ d+e++t+lvll++kd+++fpl+fYRen+aD+al+++d++e++ia++kall++gt++s++ + +a+++a
  lcl|FitnessBrowser__WCS417:GFF2324  86 DVSGIKVDPERLTALVLLGLKDRETFPLVFYRENCADMALRAEDISEAFIASSKALLITGTHFSTDGVYKASIQA 160
                                         *************************************************************************** PP

                           TIGR04382 151 lelakkagvkvvlDiDYRpvlWk............skeeasaalqlvlkkvdviiGteeEfeiaagekddeaaak 213
                                         l++a k++v+ vlDiDYRpvlW+            +++++s+++q++l+++d+i+GteeEf ia g++d  +a++
  lcl|FitnessBrowser__WCS417:GFF2324 161 LDYAAKHNVQRVLDIDYRPVLWGlagkadgetrfvADQNVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLTALR 235
                                         *************************************************************************** PP

                           TIGR04382 214 allelgaelvvvKrGeeGslvytkd.....eeevevkgfkvevlkvlGaGDaFasgllygllegedlekalelan 283
                                         +++el+++++vvK G++G++v++++     e+   ++g++vevl+vlGaGDaF+sg+l+g++++ + e++ +lan
  lcl|FitnessBrowser__WCS417:GFF2324 236 KVRELTQATLVVKLGPQGCTVIHGAiparlEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWINDASDERCSQLAN 310
                                         *****************************9999****************************************** PP

                           TIGR04382 284 Aagaivvsrlscaeamptleeleef 308
                                         A+g +vvsr++ca+ampt +ele +
  lcl|FitnessBrowser__WCS417:GFF2324 311 ACGGLVVSRHACAPAMPTPAELEYL 335
                                         *********************9975 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.47
//
[ok]

This GapMind analysis is from Sep 17 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 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