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.19408.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 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 11.77
//
[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:

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:

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:

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:

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