Alignments for a candidate for 1pfk in Maridesulfovibrio zosterae DSM 11974

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Maridesulfovibrio zosterae DSM 11974

Align 1-phosphofructokinase (EC 2.7.1.56) (characterized)
to candidate WP_027722882.1 H589_RS0115580 1-phosphofructokinase

Query= reanno::psRCH2:GFF3290
         (312 letters)



>NCBI__GCF_000425265.1:WP_027722882.1
          Length = 316

 Score =  221 bits (564), Expect = 1e-62
 Identities = 124/309 (40%), Positives = 175/309 (56%), Gaps = 1/309 (0%)

Query: 4   VLTVTLNPALDLTVQLPALRLGEVNRSDSLQVHAAGKGLNVAQVLADLGHQLTVTGFLGE 63
           ++TVT+NPA+DL  Q+P    G+VNR    Q  AAGKG+N+A +L      +TVTGFLG 
Sbjct: 7   IITVTMNPAIDLACQVPDFTAGKVNRVAGYQTDAAGKGVNIAVLLRKFDLPVTVTGFLGA 66

Query: 64  GNPQAFEQLFSARGFTDEFVRVAGETRSNLKLAEAD-GRVTDINGPGLAVSEAQRAELLA 122
            N   FE+LFS++G  DEFVRV GETR  +K+ + D G  TDIN PGL+       +L+ 
Sbjct: 67  DNALIFEKLFSSKGLKDEFVRVPGETRIGVKVLDPDSGATTDINFPGLSPDAGHVDKLMQ 126

Query: 123 RLKRLVPAHELVVVAGSLPRGIDSQWFVQLLNSLKALGVRVALDTSGAALRDGLATRPWL 182
            +  L     +VV+ GSLP  +      QL+N +K+ G +  +DTSG AL   +   P L
Sbjct: 127 TVDNLADESSIVVIGGSLPATVSPAAVGQLVNVIKSCGAKAVVDTSGPALSSAIVAVPCL 186

Query: 183 IKPNEEELAEARGIELSGSSALAAEAQRLQEEGIEHVVVSQGADGVSWFSPGAALHASPP 242
           +KPN+ EL+E  G  L     L  EA+R+   GI+ VVVS G+ G  + S      A PP
Sbjct: 187 VKPNDAELSELVGRPLKKKEELVNEARRMNRSGIDTVVVSLGSQGALFISQEEEFFAKPP 246

Query: 243 KVRVVSTVGAGDSLLAGMLHGLLEGWPAERTLTHATAIAAQAVGQVGFGITDTAQLAELQ 302
            +  VSTVGAGD+++ GM+ G+            AT+++A  V Q G  + D     EL+
Sbjct: 247 TINAVSTVGAGDAMIGGMVAGMALELSLRERACLATSLSAATVAQAGPSLEDIEIAKELE 306

Query: 303 AAVRLQPLS 311
             V ++ +S
Sbjct: 307 EQVVIETIS 315


Lambda     K      H
   0.316    0.132    0.371 

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: 239
Number of extensions: 8
Number of successful extensions: 3
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: 312
Length of database: 316
Length adjustment: 27
Effective length of query: 285
Effective length of database: 289
Effective search space:    82365
Effective search space used:    82365
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate WP_027722882.1 H589_RS0115580 (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.1624138.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.9e-100  320.4   1.7   5.6e-100  320.3   1.7    1.0  1  NCBI__GCF_000425265.1:WP_027722882.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000425265.1:WP_027722882.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  320.3   1.7  5.6e-100  5.6e-100       1     305 []       7     312 ..       7     312 .. 0.99

  Alignments for each domain:
  == domain 1  score: 320.3 bits;  conditional E-value: 5.6e-100
                             TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealleee 73 
                                           I+TvT+NpaiD++ ++ ++++g+vnrv+  ++da+GKG+n+a +L+k++ +v+++gflG++++  +e+l++++
  NCBI__GCF_000425265.1:WP_027722882.1   7 IITVTMNPAIDLACQVPDFTAGKVNRVAGYQTDAAGKGVNIAVLLRKFDLPVTVTGFLGADNALIFEKLFSSK 79 
                                           89*********************************************************************** PP

                             TIGR03828  74 giktdfvevkgetRinvkikes.sgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvpedl 145
                                           g+k++fv+v+getRi vk+ ++ sg +t++n+pG + ++ ++++l++++++ + e++++v++GSlP++v++ +
  NCBI__GCF_000425265.1:WP_027722882.1  80 GLKDEFVRVPGETRIGVKVLDPdSGATTDINFPGLSPDAGHVDKLMQTVDNLADESSIVVIGGSLPATVSPAA 152
                                           **************************************************999******************** PP

                             TIGR03828 146 yaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgvenvli 218
                                           + +l++++++ gak ++Dtsg+aL+ ++ a p+l+KPN++El+el+gr lk++ee+++ ar++ ++g++ v++
  NCBI__GCF_000425265.1:WP_027722882.1 153 VGQLVNVIKSCGAKAVVDTSGPALSSAIVAVPCLVKPNDAELSELVGRPLKKKEELVNEARRMNRSGIDTVVV 225
                                           ************************************************************************* PP

                             TIGR03828 219 slGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaassegtelpd 291
                                           slG++Gal++++e+++fak+p+i+++stvGAGD+m++g++++++ +lsl e+  la++++aa+++++g +l d
  NCBI__GCF_000425265.1:WP_027722882.1 226 SLGSQGALFISQEEEFFAKPPTINAVSTVGAGDAMIGGMVAGMALELSLRERACLATSLSAATVAQAGPSLED 298
                                           ************************************************************************* PP

                             TIGR03828 292 ledieelleevkie 305
                                           +e  +el+e+v ie
  NCBI__GCF_000425265.1:WP_027722882.1 299 IEIAKELEEQVVIE 312
                                           ***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (316 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: 14.29
//
[ok]

This GapMind analysis is from Apr 09 2024. 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 2024 update 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