Alignments for a candidate for 1pfk in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for 1pfk in Klebsiella michiganensis M5al

Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate BWI76_RS24860 BWI76_RS24860 1-phosphofructokinase

Query= curated2:O31714
         (303 letters)



>FitnessBrowser__Koxy:BWI76_RS24860
          Length = 304

 Score =  174 bits (440), Expect = 3e-48
 Identities = 96/304 (31%), Positives = 166/304 (54%), Gaps = 1/304 (0%)

Query: 1   MIYTVTLNPSVDYIVHVEDFTVGGLNRSSYDTKYPGGKGINVSRLLKRHHVASKALGFVG 60
           MI+T+TLN ++D  +  +      +NR+ +    P GKG+NVS +L  +   +  +G  G
Sbjct: 1   MIHTLTLNTAIDMNIFCDPLKPSAVNRTRHTEYCPNGKGVNVSLILNHYQQPTHIIGIFG 60

Query: 61  GFTGEYIKTFLREENLETAFSEVKGDTRINVKLKTG-DETEINGQGPTISDEDFKAFLEQ 119
           GFTG YI   LR++ ++   + V   TRIN+ +  G +E ++   G  I DE  +  +  
Sbjct: 61  GFTGRYIVEELRQKKIKVTPAWVSEPTRINIFINDGAEEYKLVNPGAKIDDECKQQVIHH 120

Query: 120 FQSLQEGDIVVLAGSIPSSLPHDTYEKIAEACKQQNARVVLDISGEALLKATEMKPFLMK 179
            Q +  GD + ++GS+P  +    Y +I E C+Q+   V+LDIS   L +  E++P L+K
Sbjct: 121 LQCVASGDYLAISGSLPPGIESRFYAEIIELCQQKRCEVILDISHPVLRQLLELRPLLIK 180

Query: 180 PNHHELGEMFGTAITSVEEAVPYGKKLVEQGAEHVIVSMAGDGALLFTNEAVYFANVPKG 239
           PN  EL E+FG  +++ ++     + L + GA +V+++M  +G      E V+F + PK 
Sbjct: 181 PNDDELREIFGLDVSNHQQVREAMRTLHQLGARNVLLTMGAEGLYFSDGEGVWFCSAPKI 240

Query: 240 KLVNSVGAGDSVVAGFLAGISKQLPLEEAFRLGVTSGSATAFSEELGTEEFVQQLLPEVK 299
            LV+S  AGD+ +  FL+    +  +  A  L   +G+  A S  LG  +  ++LL +++
Sbjct: 241 ALVSSACAGDAALGAFLSKWLNKEDVAHALALASATGADVAGSAGLGKLQRTEELLQQIQ 300

Query: 300 VTRL 303
           V +L
Sbjct: 301 VVQL 304


Lambda     K      H
   0.315    0.134    0.372 

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: 240
Number of extensions: 14
Number of successful extensions: 2
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: 303
Length of database: 304
Length adjustment: 27
Effective length of query: 276
Effective length of database: 277
Effective search space:    76452
Effective search space used:    76452
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: 42 (22.0 bits)
S2: 48 (23.1 bits)

Align candidate BWI76_RS24860 BWI76_RS24860 (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.15451.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   1.3e-100  322.3   0.0   1.5e-100  322.1   0.0    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS24860  BWI76_RS24860 1-phosphofructokin


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS24860  BWI76_RS24860 1-phosphofructokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.1   0.0  1.5e-100  1.5e-100       1     304 [.       2     301 ..       2     302 .. 0.99

  Alignments for each domain:
  == domain 1  score: 322.1 bits;  conditional E-value: 1.5e-100
                               TIGR03828   1 IlTvTlNpaiDktieleelelgevnrveserldagGKGinVarvLkklgvevvalgflGgftgeeiealle 71 
                                             I T+TlN+aiD+ i  + l++ +vnr+++++++++GKG+nV+ +L++ +++++++g++Ggftg++i ++l+
  lcl|FitnessBrowser__Koxy:BWI76_RS24860   2 IHTLTLNTAIDMNIFCDPLKPSAVNRTRHTEYCPNGKGVNVSLILNHYQQPTHIIGIFGGFTGRYIVEELR 72 
                                             88********************************************************************* PP

                               TIGR03828  72 eegiktdfvevkgetRinvkikessgeetklnepGpeiseeeleallekleeqlkegdvlvlaGSlPrgvp 142
                                             +++ik+++ +v++ tRin++i++   ee+kl++pG++i++e++++++++l+  +++gd+l ++GSlP+g++
  lcl|FitnessBrowser__Koxy:BWI76_RS24860  73 QKKIKVTPAWVSEPTRINIFIND-GAEEYKLVNPGAKIDDECKQQVIHHLQ-CVASGDYLAISGSLPPGIE 141
                                             **********************8.9**************************.9****************** PP

                               TIGR03828 143 edlyaelikllrekgakvilDtsgeaLlkvlkakplliKPNkeEleellgrelkteeevieaarkllekgv 213
                                             +++yae+i+l+++k  +vilD+s+++L++ l+ +plliKPN++El e++g +++++++v ea+r+l++ g+
  lcl|FitnessBrowser__Koxy:BWI76_RS24860 142 SRFYAEIIELCQQKRCEVILDISHPVLRQLLELRPLLIKPNDDELREIFGLDVSNHQQVREAMRTLHQLGA 212
                                             *********************************************************************** PP

                               TIGR03828 214 envlislGadGallvtkegalfakapkievkstvGAGDsmvAgfllalekglsleealrlavAvgaaaass 284
                                             +nvl+++Ga+G ++ + eg++f++apki ++s+++AGD+++++fl+++ +++++++al+la A+ga++a s
  lcl|FitnessBrowser__Koxy:BWI76_RS24860 213 RNVLLTMGAEGLYFSDGEGVWFCSAPKIALVSSACAGDAALGAFLSKWLNKEDVAHALALASATGADVAGS 283
                                             *********************************************************************** PP

                               TIGR03828 285 egtelpdledieelleevki 304
                                             +g  l++l++ eell+++++
  lcl|FitnessBrowser__Koxy:BWI76_RS24860 284 AG--LGKLQRTEELLQQIQV 301
                                             **..**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (305 nodes)
Target sequences:                          1  (304 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: 9.88
//
[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:

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