Alignments for a candidate for 1pfk in Oceanisphaera arctica V1-41

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Oceanisphaera arctica V1-41

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate WP_104485040.1 UN63_RS01630 1-phosphofructokinase

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



>NCBI__GCF_002936955.1:WP_104485040.1
          Length = 314

 Score =  278 bits (710), Expect = 2e-79
 Identities = 152/307 (49%), Positives = 196/307 (63%)

Query: 4   ILTLTLNPALDLTVELARLEPGQVNRSDAMHAHAAGKGVNVAQVLADLGHTLTVSGFLGE 63
           ILTLTLNPALDLTV L  L  G VN ++  H  AAGKG+NVA+VLADLGH    +GFLG 
Sbjct: 3   ILTLTLNPALDLTVSLKPLNTGAVNLANHGHLGAAGKGINVARVLADLGHRPRATGFLGL 62

Query: 64  DNAQVFETLFAQRGFVDAFIRVPGETRSNIKLAEQDGRITDLNGPGPMVDAAAQQALLAR 123
           +N   F  +F + G  D F+R+ G+TR N+K++E+ GR+TD+N PG  V+ +    LLAR
Sbjct: 63  NNDASFRAMFERYGIEDDFVRLAGDTRVNVKISEEGGRVTDINLPGLQVEKSDWNRLLAR 122

Query: 124 LEQIAPGHDVVVVAGSLPRGVSPQWLQALIARMKALGLNVALDTSGEALRVALAAGPWLI 183
           LE +    D +VVAGSLP GV P+ L+ LI   +  G  V LD SGE LRV +   P LI
Sbjct: 123 LESLERHFDTLVVAGSLPPGVYPKQLEGLIDMWRERGKLVLLDASGETLRVGIKGFPALI 182

Query: 184 KPNTEELADALGCEVVSETAQAQAAQRLHAQGIEHVVISHGADGVNWFSVGAALHASPPK 243
           KPN +EL D +G  +  E   A  A+ L  QGI+H+V+S+GA+GV+WFS   A  A  PK
Sbjct: 183 KPNIDELVDLVGRPIRDEADLADCARELQQQGIQHIVVSNGAEGVHWFSPRGAWKARVPK 242

Query: 244 VSVASTVGAGDSLLAGMLHGLLSADTPEQTLRTATAIAAMAVTQIGFGIHDTALLASLEQ 303
           V V STVGAGDSL+AG+  GLL       TLR A A++ MAVTQ+G GI +   L   + 
Sbjct: 243 VKVVSTVGAGDSLVAGLCAGLLEGRDEAFTLRRAVALSIMAVTQVGVGISNKQQLNDYQD 302

Query: 304 GVRVRPL 310
            + +  L
Sbjct: 303 AIEITQL 309


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: 264
Number of extensions: 7
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: 314
Length adjustment: 27
Effective length of query: 286
Effective length of database: 287
Effective search space:    82082
Effective search space used:    82082
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_104485040.1 UN63_RS01630 (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.3656734.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-101  325.0   0.0   2.3e-101  324.8   0.0    1.0  1  NCBI__GCF_002936955.1:WP_104485040.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002936955.1:WP_104485040.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  324.8   0.0  2.3e-101  2.3e-101       1     304 [.       3     306 ..       3     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: 324.8 bits;  conditional E-value: 2.3e-101
                             TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 
                                           IlT+TlNpa+D+t++l+ l++g+vn +++ +l a+GKGinVarvL++lg++  a+gflG ++ ++++a++e+ 
  NCBI__GCF_002936955.1:WP_104485040.1   3 ILTLTLNPALDLTVSLKPLNTGAVNLANHGHLGAAGKGINVARVLADLGHRPRATGFLGLNNDASFRAMFERY 75 
                                           89*********************************************************************** PP

                             TIGR03828  74 giktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedly 146
                                           gi++dfv+++g+tR+nvki+e+ g++t++n pG +++++++++ll++le+  ++ d+lv+aGSlP+gv ++ +
  NCBI__GCF_002936955.1:WP_104485040.1  76 GIEDDFVRLAGDTRVNVKISEEGGRVTDINLPGLQVEKSDWNRLLARLESLERHFDTLVVAGSLPPGVYPKQL 148
                                           *************************************************988999****************** PP

                             TIGR03828 147 aelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvlis 219
                                           + li++ re+g+ v lD+sge+L+ ++k  p liKPN +El +l+gr + +e+++ ++ar+l+++g++++++s
  NCBI__GCF_002936955.1:WP_104485040.1 149 EGLIDMWRERGKLVLLDASGETLRVGIKGFPALIKPNIDELVDLVGRPIRDEADLADCARELQQQGIQHIVVS 221
                                           ************************************************************************* PP

                             TIGR03828 220 lGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpdl 292
                                            Ga+G+ ++++ ga++a+ pk++v+stvGAGDs+vAg++++l +g +++ +lr avA++  a+++ g+++ ++
  NCBI__GCF_002936955.1:WP_104485040.1 222 NGAEGVHWFSPRGAWKARVPKVKVVSTVGAGDSLVAGLCAGLLEGRDEAFTLRRAVALSIMAVTQVGVGISNK 294
                                           ************************************************************************* PP

                             TIGR03828 293 edieelleevki 304
                                           ++++++++ ++i
  NCBI__GCF_002936955.1:WP_104485040.1 295 QQLNDYQDAIEI 306
                                           *********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (314 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 15.21
//
[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:

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