GapMind for catabolism of small carbon sources

 

Alignments for a candidate for 1pfk in Marinobacter algicola DG893

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate WP_007154190.1 MDG893_RS12695 1-phosphofructokinase

Query= reanno::pseudo5_N2C3_1:AO356_07330
         (313 letters)



>NCBI__GCF_000170835.1:WP_007154190.1
          Length = 330

 Score =  256 bits (655), Expect = 4e-73
 Identities = 146/291 (50%), Positives = 180/291 (61%)

Query: 1   MAKILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGF 60
           MA++LT+TLNPALDL  E   +  G VNRS +    AAGKG+N+ +VL  LGHT+TVSG 
Sbjct: 1   MARVLTITLNPALDLNAETDSMRLGNVNRSRSTRLEAAGKGINLGRVLTRLGHTVTVSGL 60

Query: 61  LGEDNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQAL 120
           LG+ NA  F+ LF+     D F+R+PG+ R N+K+AE  GR+TDLNGPG  V A A   L
Sbjct: 61  LGDINAAPFDRLFSSDILADHFVRIPGQNRINVKIAESGGRVTDLNGPGFDVPADALDRL 120

Query: 121 LARLEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGP 180
            ARL  +    D V +AGSLP G  P+ L  L+   +   + V LDTSG  L   L A P
Sbjct: 121 KARLGDLKSRFDAVAIAGSLPGGFPPEALAELVTLAREADIPVWLDTSGAGLTAGLKALP 180

Query: 181 WLIKPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHAS 240
             IKPN EELA+  G  + S  A A+A + L A GI +VVIS G  GV W S      A 
Sbjct: 181 DGIKPNMEELAEWAGHPLESLDAIAEAGRSLQATGIANVVISMGEKGVLWLSPKGNWQAL 240

Query: 241 PPKVSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFG 291
           PP V+  STV AGD+LLAGM+HGLL    PEQ L TATA++A  V  IG G
Sbjct: 241 PPPVTATSTVCAGDTLLAGMIHGLLEHHHPEQVLSTATALSAECVRHIGVG 291


Lambda     K      H
   0.317    0.132    0.373 

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: 300
Number of extensions: 11
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: 313
Length of database: 330
Length adjustment: 28
Effective length of query: 285
Effective length of database: 302
Effective search space:    86070
Effective search space used:    86070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate WP_007154190.1 MDG893_RS12695 (1-phosphofructokinase)
to HMM TIGR03828 (pfkB: 1-phosphofructokinase (EC 2.7.1.56))

# 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/TIGR03828.hmm
# target sequence database:        /tmp/gapView.3428827.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03828  [M=305]
Accession:   TIGR03828
Description: pfkB: 1-phosphofructokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    6.2e-95  303.7   0.0    7.2e-95  303.5   0.0    1.0  1  NCBI__GCF_000170835.1:WP_007154190.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000170835.1:WP_007154190.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  303.5   0.0   7.2e-95   7.2e-95       1     304 [.       4     307 ..       4     308 .. 0.98

  Alignments for each domain:
  == domain 1  score: 303.5 bits;  conditional E-value: 7.2e-95
                             TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 
                                           +lT+TlNpa+D+  e+++++lg+vnr +s+rl+a+GKGin  rvL++lg++v+++g+lG  +++++++l++++
  NCBI__GCF_000170835.1:WP_007154190.1   4 VLTITLNPALDLNAETDSMRLGNVNRSRSTRLEAAGKGINLGRVLTRLGHTVTVSGLLGDINAAPFDRLFSSD 76 
                                           79*********************************************************************** PP

                             TIGR03828  74 giktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedly 146
                                            ++++fv+++g+ Rinvki+es g++t+ln+pG+ + +++l++l+++l +  ++ d + +aGSlP g p++++
  NCBI__GCF_000170835.1:WP_007154190.1  77 ILADHFVRIPGQNRINVKIAESGGRVTDLNGPGFDVPADALDRLKARLGDLKSRFDAVAIAGSLPGGFPPEAL 149
                                           *************************************************99999******************* PP

                             TIGR03828 147 aelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlis 219
                                           ael+ l+re++++v lDtsg+ L+++lka p+ iKPN eEl+e++g+ l++ +++ ea+r l++ g++nv+is
  NCBI__GCF_000170835.1:WP_007154190.1 150 AELVTLAREADIPVWLDTSGAGLTAGLKALPDGIKPNMEELAEWAGHPLESLDAIAEAGRSLQATGIANVVIS 222
                                           ************************************************************************* PP

                             TIGR03828 220 lGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpdl 292
                                           +G++G+l+++++g ++a +p +++ stv+AGD+++Ag++++l +++++e++l++a+A++a+ + + g++ p  
  NCBI__GCF_000170835.1:WP_007154190.1 223 MGEKGVLWLSPKGNWQALPPPVTATSTVCAGDTLLAGMIHGLLEHHHPEQVLSTATALSAECVRHIGVGDPMA 295
                                           *******************************************************************888888 PP

                             TIGR03828 293 edieelleevki 304
                                           +d  +l +++++
  NCBI__GCF_000170835.1:WP_007154190.1 296 DDFIQLIQQTRV 307
                                           888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (330 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.28
//
[ok]

This GapMind analysis is from Sep 24 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