Alignments for a candidate for galK in Pseudarthrobacter sulfonivorans Ar51

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Pseudarthrobacter sulfonivorans Ar51

Align Galactokinase; EC 2.7.1.6; Galactose kinase (uncharacterized)
to candidate WP_058932741.1 AU252_RS04315 galactokinase

Query= curated2:P13227
         (397 letters)



>NCBI__GCF_001484605.1:WP_058932741.1
          Length = 387

 Score =  308 bits (788), Expect = 2e-88
 Identities = 179/366 (48%), Positives = 221/366 (60%), Gaps = 4/366 (1%)

Query: 18  GRSRRGCGRRAGRENLIGEHTDYNDGFVMPSALPHQV-AAVSRRERRILRLHSADVDADP 76
           GR   G  +  GR NLIGEHTDYN+GFV+P A+      AV  R    +RL S   D   
Sbjct: 20  GRLPDGVWQAPGRVNLIGEHTDYNEGFVLPFAIDKTARVAVGVRPDSTVRLLSTYGDHGM 79

Query: 77  VELRVADLAPASDKSWTAYPSGVLWALREAGHELTGADVHLASTVPSGAGLSSSAALEVR 136
           V   +  L  AS K WT YP GV+WAL++ G  + G D+ L S VP GAGLSSS A+E  
Sbjct: 80  VTADLGSLDAASAKGWTKYPLGVMWALQQQGIAVPGVDLLLDSNVPLGAGLSSSHAIECA 139

Query: 137 PL-AMNDLYALALRGWQLARLCQRAENVYVGAPVGIMDQTASACCRGGHALFLDTRDLSQ 195
            + A+NDL    L   ++    QRAEN +VGAP GIMDQ+AS     GHA+FLD RD S 
Sbjct: 140 VISALNDLTGAGLEPEEMVLATQRAENDFVGAPTGIMDQSASLRGSKGHAVFLDCRDQSV 199

Query: 196 RQIPFDLAAEGMRLLVVDTRVKHSHSEGEYGKRRAGCEKGAALLGVDALCDVPYADLDAA 255
           + +PF+    G+ +LV+DT V HSH++G Y  RRA CE GA +LGV AL DV   DL+ A
Sbjct: 200 QLVPFETEPAGLVMLVIDTNVSHSHADGGYASRRASCELGAEVLGVKALRDVRMEDLEEA 259

Query: 256 LERLGDEEEVRRLVRHVVTEDERVERVVALLESGDTRRIGAVLVEGHASLRDDFRISCPE 315
              L  +E   R VRH+VTE++RV + V LL S     IGA+L   H S+RDDF ISCPE
Sbjct: 260 AGLL--DEVTYRRVRHIVTENDRVLQTVELLASAGPGSIGALLDASHVSMRDDFEISCPE 317

Query: 316 LDLVVDTALASAALGRRMTGGGFGGSAIVLVEAAAVDAVTKAVEDAFAAAGLKRPRVFEA 375
           LDL V T+ A+ A+G RMTGGGFGG+AI L    +   V  AV  AF  AG   P +F  
Sbjct: 318 LDLAVATSRANGAIGARMTGGGFGGAAIALTPVTSEQQVRAAVVRAFEEAGYTAPDIFTV 377

Query: 376 VPRRGA 381
            P  GA
Sbjct: 378 TPAAGA 383


Lambda     K      H
   0.319    0.134    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: 370
Number of extensions: 16
Number of successful extensions: 4
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: 397
Length of database: 387
Length adjustment: 31
Effective length of query: 366
Effective length of database: 356
Effective search space:   130296
Effective search space used:   130296
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 WP_058932741.1 AU252_RS04315 (galactokinase)
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.26734.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    3.5e-97  311.7   0.0    4.2e-97  311.4   0.0    1.0  1  lcl|NCBI__GCF_001484605.1:WP_058932741.1  AU252_RS04315 galactokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001484605.1:WP_058932741.1  AU252_RS04315 galactokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.4   0.0   4.2e-97   4.2e-97       4     370 ..      11     368 ..       8     385 .. 0.92

  Alignments for each domain:
  == domain 1  score: 311.4 bits;  conditional E-value: 4.2e-97
                                 TIGR00131   4 vkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnkl 72 
                                               +   F + ++  pd v +aPGRvnliGeh+DYn+g+vlP aid    vav +r d +v++ ++  d  +
  lcl|NCBI__GCF_001484605.1:WP_058932741.1  11 LAARFEQEFGRLPDGVWQAPGRVNLIGEHTDYNEGFVLPFAIDKTARVAVGVRPDSTVRLLSTYGDHGM 79 
                                               56789**************************************************************** PP

                                 TIGR00131  73 aerkldlpldksevsdWanYvkgvlkvlqeRfnsvplGldivisgdvPtgaGLsssaalevavaavlkn 141
                                                   l     +s  + W+ Y+ gv+  lq+   +vp G+d++++++vP gaGLsss a+e+av   l++
  lcl|NCBI__GCF_001484605.1:WP_058932741.1  80 VTADLGSLDAASA-KGWTKYPLGVMWALQQQGIAVP-GVDLLLDSNVPLGAGLSSSHAIECAVISALND 146
                                               9999987666666.9*********************.******************************** PP

                                 TIGR00131 142 lgkleldskeillriqkveehfvGvncGgmDqlasvlGeedhallvefr..kLkatpvklpqleialvi 208
                                               l    l+ +e++l +q++e+ fvG+ +G+mDq as  G + ha+++++r  +++  p++ +  ++ +++
  lcl|NCBI__GCF_001484605.1:WP_058932741.1 147 LTGAGLEPEEMVLATQRAENDFVGAPTGIMDQSASLRGSKGHAVFLDCRdqSVQLVPFETEPAGLVMLV 215
                                               *************************************************54455555555556****** PP

                                 TIGR00131 209 antnvksnlapseYnlRrqeveeaakvlakksekgaLrDvkeeefaryearltkllqlvekqRakhvvs 277
                                               ++tnv +  a++ Y  Rr  +e +a+vl +k    aLrDv  e+ +   + +  ll +v  +R++h+v+
  lcl|NCBI__GCF_001484605.1:WP_058932741.1 216 IDTNVSHSHADGGYASRRASCELGAEVLGVK----ALRDVRMEDLE---E-AAGLLDEVTYRRVRHIVT 276
                                               *******************************....*********99...5.55555566666******* PP

                                 TIGR00131 278 enlRvlkavkllkdedlkelGkLmnesqasldddyeitvpeidelvesialvnGsiGsRltGaGfGGCt 346
                                               en Rvl++v+ll      ++G+L+++s+ s++dd+ei++pe+d l ++   +nG iG+R+tG+GfGG  
  lcl|NCBI__GCF_001484605.1:WP_058932741.1 277 ENDRVLQTVELLASAGPGSIGALLDASHVSMRDDFEISCPELD-LAVATSRANGAIGARMTGGGFGGAA 344
                                               *******************************************.8888899****************** PP

                                 TIGR00131 347 valvpnenvekvrkalaekYekkt 370
                                               +al p    ++vr a++  +e+  
  lcl|NCBI__GCF_001484605.1:WP_058932741.1 345 IALTPVTSEQQVRAAVVRAFEEAG 368
                                               *****99999*****999988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (387 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: 8.00
//
[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