Alignments for a candidate for iolC in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolC in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_4274 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain

Query= reanno::pseudo3_N2E3:AO353_21335
         (645 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274
          Length = 645

 Score = 1233 bits (3189), Expect = 0.0
 Identities = 612/645 (94%), Positives = 632/645 (97%)

Query: 1   MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLK 60
           MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLK
Sbjct: 1   MGQTRFASGRQLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLK 60

Query: 61  SAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGLKDRETFPLVFYRENC 120
           SAMLSRVGDDHMGRFLVESL REGCDVSGIKVDPERLTAMVLLGLKDRETFPLVFYRENC
Sbjct: 61  SAMLSRVGDDHMGRFLVESLTREGCDVSGIKVDPERLTAMVLLGLKDRETFPLVFYRENC 120

Query: 121 ADMALRAEDISEAFIASSKALLITGTHFSTDGVYKASIQALEYAEKHNVKRILDIDYRPV 180
           ADMALRAEDI+EAFIASSKALLITGTHFSTDGVYKASIQAL+YAEKHNVKR+LDIDYRPV
Sbjct: 121 ADMALRAEDINEAFIASSKALLITGTHFSTDGVYKASIQALDYAEKHNVKRVLDIDYRPV 180

Query: 181 LWGLAGKADGETRFVADQQVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLSALRNVRRL 240
           LWGLAGKADGETRFVADQ VSQHVQKILPRFDLIVGTEEEFLIAGGSEDLL+AL+NVRRL
Sbjct: 181 LWGLAGKADGETRFVADQNVSQHVQKILPRFDLIVGTEEEFLIAGGSEDLLTALQNVRRL 240

Query: 241 TAATLVVKLGPQGCTVIHGVIPVRLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWLEDA 300
           +AATLVVKLGPQGCTVIHG IP RLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWLEDA
Sbjct: 241 SAATLVVKLGPQGCTVIHGAIPARLEDGAIYPGVRVEVLNVLGAGDAFMSGFLSGWLEDA 300

Query: 301 SDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFNSPVPITRPDQDAVLQRLHQVSVP 360
           SDERCCQLANACG LVVSRHACAPAMPTRAELDYLFNSPVPITRPDQDAVLQRLHQVSVP
Sbjct: 301 SDERCCQLANACGALVVSRHACAPAMPTRAELDYLFNSPVPITRPDQDAVLQRLHQVSVP 360

Query: 361 RKTWKQLFIFAFDHRGQLVELAQKGGRELSSIGELKQLFIKAVERVEADLRRQGIEADVG 420
           RK WKQLFIFAFDHRGQLVELA KGGR+LSSIGELKQLFIKAVERVEADLR QG++ADVG
Sbjct: 361 RKQWKQLFIFAFDHRGQLVELAHKGGRDLSSIGELKQLFIKAVERVEADLREQGVDADVG 420

Query: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480
           LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ
Sbjct: 421 LLADQRFGQDSLNAATGRGWWVARPVEVQGSRPLAFEHGRSIGSNLIAWPQEQIIKCLVQ 480

Query: 481 FHPDDEPLLRLEQEAQIKGLYQAAQVSGHELLLEIIPPKDHPSAHPDVLYRAIKRLYNLG 540
           FHPDDEPLLRLEQEAQIKGLYQA+QVSGHELLLEIIPPKDHPS HPDVLYRA+KRLY+LG
Sbjct: 481 FHPDDEPLLRLEQEAQIKGLYQASQVSGHELLLEIIPPKDHPSQHPDVLYRALKRLYSLG 540

Query: 541 IFPAWWKIEAQSSEEWKQLDDLIQERDPYCRGVVLLGLNAPAATLAEGFAQASQSKTCRG 600
           I+PAWWKIEAQS+EEWKQLD+LIQERDPYCRGVVLLGLNAPAA LAEGF QASQS+TCRG
Sbjct: 541 IYPAWWKIEAQSAEEWKQLDELIQERDPYCRGVVLLGLNAPAAALAEGFQQASQSQTCRG 600

Query: 601 FAVGRTIFQEPSRAWLAGEIDDEALIQRVQGTFVELINAWRTARA 645
           FAVGRTIFQEPSRAW+AGEIDDE LI++VQGTFVELI+AW TARA
Sbjct: 601 FAVGRTIFQEPSRAWMAGEIDDETLIRQVQGTFVELIDAWCTARA 645


Lambda     K      H
   0.321    0.138    0.412 

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: 1415
Number of extensions: 37
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 Pf1N1B4_4274 (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.14346.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   1.9e-126  407.5   0.0   2.5e-126  407.1   0.0    1.2  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274  5-keto-2-deoxygluconokinase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274  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 !  407.1   0.0  2.5e-126  2.5e-126       1     308 [.      11     335 ..      11     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 407.1 bits;  conditional E-value: 2.5e-126
                                      TIGR04382   1 kldlitiGRvgvDlyaqqigasledvksfakylGGspaNiavgaarlGlktalitkvgddqlGr 64 
                                                    +ldli++GR+gvDlyaqq+ga+ledv+sfakylGGs+aNia+g+arlGlk+a++++vgdd++Gr
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274  11 QLDLICLGRLGVDLYAQQVGARLEDVSSFAKYLGGSSANIAFGTARLGLKSAMLSRVGDDHMGR 74 
                                                    68************************************************************** PP

                                      TIGR04382  65 fvreeleregvdtshvvtdkeartslvlleikdpdefpllfYRenaaDlaltvddvdeeliaea 128
                                                    f+ e+l+reg+d+s+++ d+e++t++vll++kd+++fpl+fYRen+aD+al+++d++e++ia++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274  75 FLVESLTREGCDVSGIKVDPERLTAMVLLGLKDRETFPLVFYRENCADMALRAEDINEAFIASS 138
                                                    **************************************************************** PP

                                      TIGR04382 129 kallvsgtalskepsreavlkalelakkagvkvvlDiDYRpvlWk............skeeasa 180
                                                    kall++gt++s++ + +a+++al++a k++vk vlDiDYRpvlW+            +++++s+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274 139 KALLITGTHFSTDGVYKASIQALDYAEKHNVKRVLDIDYRPVLWGlagkadgetrfvADQNVSQ 202
                                                    **************************************************************** PP

                                      TIGR04382 181 alqlvlkkvdviiGteeEfeiaagekddeaaakallelgaelvvvKrGeeGslvytkd.....e 239
                                                    ++q++l+++d+i+GteeEf ia g++d  +a++++++l+a+++vvK G++G++v++++     e
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274 203 HVQKILPRFDLIVGTEEEFLIAGGSEDLLTALQNVRRLSAATLVVKLGPQGCTVIHGAiparlE 266
                                                    **************************************************************99 PP

                                      TIGR04382 240 eevevkgfkvevlkvlGaGDaFasgllygllegedlekalelanAagaivvsrlscaeamptle 303
                                                    +   ++g++vevl+vlGaGDaF+sg+l+g+le+ + e++++lanA+ga+vvsr++ca+ampt +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274 267 DGAIYPGVRVEVLNVLGAGDAFMSGFLSGWLEDASDERCCQLANACGALVVSRHACAPAMPTRA 330
                                                    99************************************************************** PP

                                      TIGR04382 304 eleef 308
                                                    el+ +
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4274 331 ELDYL 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.90
//
[ok]

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

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Steps (tab-delimited)
Rules (tab-delimited)
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