Alignments for a candidate for galK in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Bacteroides thetaiotaomicron VPI-5482

Align Galactokinase (EC 2.7.1.6) (characterized)
to candidate 349898 BT0370 galactokinase (NCBI ptt file)

Query= reanno::Pedo557:CA265_RS06125
         (383 letters)



>FitnessBrowser__Btheta:349898
          Length = 384

 Score =  333 bits (854), Expect = 5e-96
 Identities = 170/381 (44%), Positives = 239/381 (62%), Gaps = 3/381 (0%)

Query: 1   MNAQHLKNTFKKLFNAEP-ILVRSPGRINIIGEHTDYNGGFVMPAAIDKAIYVAISKRGD 59
           M+ +H+++ F K F+     +  SPGRIN+IGEHTDYNGGFV P A+DK +   I   G 
Sbjct: 1   MDIEHVRSRFIKHFDGTTGFIYASPGRINLIGEHTDYNGGFVFPGAVDKGMLAEIKPNGT 60

Query: 60  DEIHLFSESYQQFDISSINSLKKSENSWANYILGIADQLKERGYQLGGFNFYIDGDVPLG 119
           D++  +S   + +    +N       SWA YI G+  ++ +RG  + GFN    GDVPLG
Sbjct: 61  DKVRAYSIDLKDYVEFGLNEEDAPRASWARYIFGVCREMIKRGVDVKGFNTAFSGDVPLG 120

Query: 120 AGLSSSAAVECATGFALDQLFSLS-VSRMDIALIAQKAEQTFAGVNCGIMDQFASVFGKK 178
           AG+SSSAA+E    FAL++LF    + + ++A + Q  E  + GVNCGIMDQFASVFGK 
Sbjct: 121 AGMSSSAALESTYAFALNELFGEGKIDKFELAKVGQATEHNYCGVNCGIMDQFASVFGKA 180

Query: 179 DQAIMLDCRSMKHIYIPLKLDGYKLLLLNTNVKHALADSAYNKRRSQCEQGVAWVKAHYP 238
              I LDCRS+++ Y P   +GY+L+L+++ VKH LA SAYNKRR  CE  VA ++  +P
Sbjct: 181 GSLIRLDCRSLEYQYFPFHPEGYRLVLMDSVVKHELASSAYNKRRQSCEAAVAAIQKKHP 240

Query: 239 NVSTLRDVDLTMLETYVKPMDLEVYNKCRFVVEEIGRLLTAAEQLENGNLQALGKLMFET 298
           +V  LRD  + MLE     ++ E Y +  +V+EEI R+L   + LE  + + +G+ M+ET
Sbjct: 241 HVEFLRDCTMDMLEEAKADINAEDYMRAEYVIEEIQRVLDVCDALEKDDYETVGQKMYET 300

Query: 299 HEGLSKDYEVSCKELDFLVEAVKPLDYVLGARMMGGGFGGCTINIVKEEKIADLVEELSS 358
           H G+SK YEVSC+ELDFL +  K    V G+R+MGGGFGGCTIN+VK E   + VE+   
Sbjct: 301 HHGMSKLYEVSCEELDFLNDCAKEYG-VTGSRVMGGGFGGCTINLVKNELYDNFVEKTKE 359

Query: 359 KYLLQFGLKLDSYTVQTDNGT 379
            +  +FG     Y V   +G+
Sbjct: 360 AFKAKFGRSPKVYDVVIGDGS 380


Lambda     K      H
   0.319    0.136    0.393 

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: 408
Number of extensions: 15
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: 383
Length of database: 384
Length adjustment: 30
Effective length of query: 353
Effective length of database: 354
Effective search space:   124962
Effective search space used:   124962
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 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate 349898 BT0370 (galactokinase (NCBI ptt file))
to HMM TIGR00131 (galK: galactokinase (EC 2.7.1.6))

# 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/TIGR00131.hmm
# target sequence database:        /tmp/gapView.14580.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00131  [M=388]
Accession:   TIGR00131
Description: gal_kin: galactokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    7.6e-94  300.7   0.1    8.5e-94  300.5   0.1    1.0  1  lcl|FitnessBrowser__Btheta:349898  BT0370 galactokinase (NCBI ptt f


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:349898  BT0370 galactokinase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.5   0.1   8.5e-94   8.5e-94       2     387 ..       4     382 ..       3     383 .. 0.93

  Alignments for each domain:
  == domain 1  score: 300.5 bits;  conditional E-value: 8.5e-94
                          TIGR00131   2 eevkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnklaerkl 77 
                                        e+v++ F++ ++   +++  +PGR+nliGeh+DYn+g+v+P a+d ++l+ +k     +v+ ++++++ +  e+ l
  lcl|FitnessBrowser__Btheta:349898   4 EHVRSRFIKHFDGTTGFIYASPGRINLIGEHTDYNGGFVFPGAVDKGMLAEIKPNGTDKVRAYSIDLK-DYVEFGL 78 
                                        678999*************************************************************9.6677888 PP

                          TIGR00131  78 dlpldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlk.nlgkleldskei 152
                                        + +   +    Wa Y+ gv +++ +R  +v+ G++  +sgdvP gaG+sssaale   a  l+  +g+++ d+ e 
  lcl|FitnessBrowser__Btheta:349898  79 NEEDAPR--ASWARYIFGVCREMIKRGVDVK-GFNTAFSGDVPLGAGMSSSAALESTYAFALNeLFGEGKIDKFEL 151
                                        7765555..59*******************9.***************************88883556778888899 PP

                          TIGR00131 153 llriqkveehfvGvncGgmDqlasvlGeedhallvefrkLkatpvklpqleialviantnvksnlapseYnlRrqe 228
                                        ++ +q+ e ++ GvncG+mDq+asv+G+   ++ +++r+L+++++++   +  lv++++ vk++la+s Yn Rrq 
  lcl|FitnessBrowser__Btheta:349898 152 AKVGQATEHNYCGVNCGIMDQFASVFGKAGSLIRLDCRSLEYQYFPFHPEGYRLVLMDSVVKHELASSAYNKRRQS 227
                                        9999*******************************************999************************** PP

                          TIGR00131 229 veeaakvlakks.ekgaLrDvkeeefaryearltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmne 303
                                        +e a+ +++kk  +   LrD +    +   +    ++ +    Ra +v+ e +Rvl+  ++l+++d +++G+ m e
  lcl|FitnessBrowser__Btheta:349898 228 CEAAVAAIQKKHpHVEFLRDCTMDMLE---EAKADINAEDYM-RAEYVIEEIQRVLDVCDALEKDDYETVGQKMYE 299
                                        ********9995155679999998888...666677776665.********************************* PP

                          TIGR00131 304 sqasldddyeitvpeidelvesialvnGsiGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavi 379
                                         +  + ++ye+++ e+d  +   a+  G++GsR+ G+GfGGCt++lv+ne  +++ ++  e +++k +   + + +
  lcl|FitnessBrowser__Btheta:349898 300 THHGMSKLYEVSCEELD-FLNDCAKEYGVTGSRVMGGGFGGCTINLVKNELYDNFVEKTKEAFKAKFGRSPKVYDV 374
                                        *****************.88999999***************************************99999999988 PP

                          TIGR00131 380 vskealge 387
                                        v++++ ++
  lcl|FitnessBrowser__Btheta:349898 375 VIGDGSRK 382
                                        88888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (384 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.58
//
[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