Alignments for a candidate for galK in Frankia alni ACN14A

GapMind for catabolism of small carbon sources

Alignments for a candidate for galK in Frankia alni ACN14A

Align Galactokinase; EC 2.7.1.6; Galactose kinase (uncharacterized)
to candidate WP_011606705.1 FRAAL_RS24495 galactokinase

Query= curated2:A7NI09
         (391 letters)



>NCBI__GCF_000058485.1:WP_011606705.1
          Length = 408

 Score =  264 bits (675), Expect = 3e-75
 Identities = 172/399 (43%), Positives = 228/399 (57%), Gaps = 40/399 (10%)

Query: 11  FQQHYGIHPSVIVRAPGRVNLIGEHTDYNDGFVFPVAIDRATYVAARLRHDQLVRVASSD 70
           F   +G  P+++VR+P RVNLIGEHTDYNDG   PVAIDR   +A R   D     A +D
Sbjct: 11  FVAAHGREPTLLVRSPARVNLIGEHTDYNDGLCLPVAIDRELCIALRRTDDV---AAGAD 67

Query: 71  ---------LNEED-TFAIDQIER--SNRP-------WHNYIRGVALALRVAGHPLL--- 108
                    ++E+D T A+ ++    ++ P       W  Y++GVA+ L  +G       
Sbjct: 68  PAAGAHLRLVSEQDPTPAVIELPPPPADTPPSARATGWTRYVQGVAVQLAASGQLAASGQ 127

Query: 109 --GADLL-----IASDVPRGAGLSSSAALEVAVGYAFQVLNNLNILGEELALLAQGAENN 161
             GADL+     +ASD+P GAGLSSSAALE+AV  A   L        ELA LAQ AEN 
Sbjct: 128 PAGADLVPWQGALASDIPLGAGLSSSAALELAVAVACTHLAGSVPAPTELARLAQRAENA 187

Query: 162 FVGVQCGIMDQLIAVLGRADHALLIDCRDLSYRAVPLPPSVAVVICDSHIPRTLAASAYN 221
           +VG   G++DQL  V G A HAL IDCR L+   VPLP  +AVV+ D+   R L  SAY 
Sbjct: 188 WVGAATGLLDQLACVGGIAGHALRIDCRTLTVTPVPLPAGLAVVVIDTGSRRELVTSAYA 247

Query: 222 QRRQECDMAVQLLRRWYPGIRALRDVSEDHLAAHSDALPEPIR-SRARHVVRENRRTLQG 280
            RR EC+ A + L     G+ ALRD+  D L A + +  +P+   RAR V+ EN R    
Sbjct: 248 DRRAECERAARAL-----GVPALRDL--DALPADAASRLDPVALRRARFVIAENARVDAV 300

Query: 281 AEALERGDVVTFGRLMNESHASLRDDYQVSLPDIDILVETAHHLAGCYGSRLTGAGFGGC 340
           AEAL RGD    GRL+   H  +RDD++VS P++D  V  A+   GC+G+R+TG GF GC
Sbjct: 301 AEALTRGDAEAAGRLLLAGHRGIRDDFEVSGPELDAAVAAAYAAPGCFGARMTGGGFAGC 360

Query: 341 TVSLVERNEVESFSRDLLRVYHNATGRTATIYVCRASDG 379
            V+LV+R  +E+F+      Y   TGR A ++VC A  G
Sbjct: 361 AVALVDRARLEAFTETFEPAYFARTGREAVLHVCSAVAG 399


Lambda     K      H
   0.322    0.137    0.405 

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: 398
Number of extensions: 20
Number of successful extensions: 5
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: 391
Length of database: 408
Length adjustment: 31
Effective length of query: 360
Effective length of database: 377
Effective search space:   135720
Effective search space used:   135720
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate WP_011606705.1 FRAAL_RS24495 (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.10231.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.6e-84  270.0   0.0    2.9e-84  269.1   0.0    1.4  1  lcl|NCBI__GCF_000058485.1:WP_011606705.1  FRAAL_RS24495 galactokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000058485.1:WP_011606705.1  FRAAL_RS24495 galactokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.1   0.0   2.9e-84   2.9e-84       4     384 ..       7     399 ..       4     403 .. 0.89

  Alignments for each domain:
  == domain 1  score: 269.1 bits;  conditional E-value: 2.9e-84
                                 TIGR00131   4 vkkiFasaykekpdlvvraPGRvnliGehiDYndgsvlPlaidvdtlvavkerddknvsitlanadnkl 72 
                                               ++++F+ a++ +p+l vr+P RvnliGeh+DYndg  lP+aid ++ +a +  dd       a a  +l
  lcl|NCBI__GCF_000058485.1:WP_011606705.1   7 AVRAFVAAHGREPTLLVRSPARVNLIGEHTDYNDGLCLPVAIDRELCIALRRTDDVAAGADPA-AGAHL 74 
                                               6789***********************************************999965543322.22233 PP

                                 TIGR00131  73 aerkldlpldksev..............sdWanYvkgvlkvlq....eRfnsvplGldiv.....isgd 118
                                                 ++ ++p  +                 + W+ Yv+gv  +l        +  p G+d+v     + +d
  lcl|NCBI__GCF_000058485.1:WP_011606705.1  75 RLVSEQDPTPAVIElppppadtppsaraTGWTRYVQGVAVQLAasgqLAASGQPAGADLVpwqgaLASD 143
                                               33343444433333677777778888889********987776565333444556***9866666789* PP

                                 TIGR00131 119 vPtgaGLsssaalevavaavlknlgkleldskeillriqkveehfvGvncGgmDqlasvlGeedhallv 187
                                               +P gaGLsssaale+ava+ + +l  +    +e +  +q++e+ +vG+ +G +Dqla v G   hal +
  lcl|NCBI__GCF_000058485.1:WP_011606705.1 144 IPLGAGLSSSAALELAVAVACTHLAGSVPAPTELARLAQRAENAWVGAATGLLDQLACVGGIAGHALRI 212
                                               ********************************************************************* PP

                                 TIGR00131 188 efrkLkatpvklpqleialviantnvksnlapseYnlRrqeveeaakvlakksekgaLrDvkeeefary 256
                                               ++r+L  tpv+lp  ++a+v+++t  +++l++s Y  Rr e+e aa++l +     aLrD+     +  
  lcl|NCBI__GCF_000058485.1:WP_011606705.1 213 DCRTLTVTPVPLPA-GLAVVVIDTGSRRELVTSAYADRRAECERAARALGVP----ALRDLDALPAD-- 274
                                               **************.*************************************....*****988777.. PP

                                 TIGR00131 257 earltkllqlvekqRakhvvsenlRvlkavkllkdedlkelGkLmnesqasldddyeitvpeidelves 325
                                                  +++l++++ + Ra+ v++en+Rv   +++l+ +d +  G+L+ + +  ++dd+e++ pe+d  v +
  lcl|NCBI__GCF_000058485.1:WP_011606705.1 275 --AASRLDPVALR-RARFVIAENARVDAVAEALTRGDAEAAGRLLLAGHRGIRDDFEVSGPELDAAVAA 340
                                               ..78999998888.******************************************************* PP

                                 TIGR00131 326 ialvnGsiGsRltGaGfGGCtvalvpnenvekvrkalaekYekktdlklefavivskea 384
                                               + ++ G +G+R+tG+Gf GC valv    +e++ ++    Y + t+ ++   v+ +  +
  lcl|NCBI__GCF_000058485.1:WP_011606705.1 341 AYAAPGCFGARMTGGGFAGCAVALVDRARLEAFTETFEPAYFARTGREAVLHVCSAVAG 399
                                               *************************************************9999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (388 nodes)
Target sequences:                          1  (408 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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 3.45
//
[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