Alignments for a candidate for galT in Lentibacillus jeotgali Grbi

GapMind for catabolism of small carbon sources

Alignments for a candidate for galT in Lentibacillus jeotgali Grbi

Align Galactose-1-phosphate uridylyltransferase; Gal-1-P uridylyltransferase; EC 2.7.7.12; UDP-glucose--hexose-1-phosphate uridylyltransferase (uncharacterized)
to candidate WP_010531699.1 ON01_RS14025 UDP-glucose--hexose-1-phosphate uridylyltransferase

Query= curated2:Q0ST91
         (498 letters)



>NCBI__GCF_000224785.1:WP_010531699.1
          Length = 493

 Score =  507 bits (1305), Expect = e-148
 Identities = 254/498 (51%), Positives = 343/498 (68%), Gaps = 13/498 (2%)

Query: 3   NLNALIDRLIEISKNNNLIEDMDTVYTRNRLLSIF--NENSYTPCEEKLTLSFHETLNEL 60
           ++NALID+ I+    + LIE  D +Y RN+++     + +  T        S  + L+EL
Sbjct: 5   HINALIDKAIQ----SGLIEKQDHIYVRNQIMHYLKLDGDKGTGSMSHSDASIPDLLDEL 60

Query: 61  INIAIEKKIIENALYSKDIFSSDIMNIFLPTPSLINKEFYKRYAISPKESTDYFYSLSKS 120
           +  A+   +I++    K+I +++IMN F+  PS+IN  F ++Y+ SP+ +TDYFY LSK 
Sbjct: 61  VAYAVRHHVIDDVFDDKEILAANIMNCFVARPSVINAVFQEKYSKSPEAATDYFYQLSKD 120

Query: 121 SNYIRTDRIAKNINFKAPSKYGTMDITINLSKPEKDPKEIALARNSVKS-NYPKCLLCIE 179
           SNYI+  RI KNI+FKA ++YG +DITINLSKPEKDP++I   R + K  +YPKC+LC+E
Sbjct: 121 SNYIQMKRIEKNIHFKANTEYGDLDITINLSKPEKDPEQIKRERENTKHIDYPKCVLCVE 180

Query: 180 NEGYEGTVTHPDRANHRMIRLSLNDRTWMLQYSPYLYYNEHCIILSEDHVPMKIDISTFK 239
           NEGY G + +P RANHR+I + L    W LQYSPY+YYNEH I+L+E H  MKID   F+
Sbjct: 181 NEGYAGRIGYPARANHRVIEVPLLGEKWYLQYSPYVYYNEHSIVLAEKHRNMKIDKQGFE 240

Query: 240 NLLSFVDKFPHYFAGSNADLPIVGGSILSHEHYQGGNHRFPMNDAKKLFDFSIDGFEDVE 299
            LL+F+DKFPHYF GSNADLPI+GGSILSH+HYQGG +RF M DA++ F F +D  ++V 
Sbjct: 241 RLLAFIDKFPHYFIGSNADLPIIGGSILSHDHYQGGRYRFAMTDAEEAFSFELDNHDNVT 300

Query: 300 CEAIKWPISTIRLRGENIDSLVLASDLILKKWRDYSDETLDILSYSNSEMHNTITPMVRK 359
            + + WP+S IRL   +   L+ A+D +L+ W+ YSDE++DI ++S +  HNTITP+ R 
Sbjct: 301 AQVLNWPLSVIRLNCSDKKELLDAADHVLQTWKHYSDESIDIKAFSGNTPHNTITPIARM 360

Query: 360 EDGKFVVDLSLRNNRTSKEHPLGIFHPHEEVHHIKKENIGLIEVMGLAVLPGRLLKELEK 419
            +G + +DL LRNNRTS+EHP+GIFHPH +VHHIKKENIGLIEVMGLAVLP RL  EL +
Sbjct: 361 RNGAYELDLVLRNNRTSEEHPMGIFHPHSDVHHIKKENIGLIEVMGLAVLPPRLKDELAE 420

Query: 420 IKEYLRDEISLDNIEEYHRPWALELKKKFDYLKSATDLNDFVNKELSNKFVSVLEHCGVF 479
           IKE+L D+ S  NIEEYH  WA  +K K   + + +D    + +EL  KF  VLE  GVF
Sbjct: 421 IKEFLLDKPS--NIEEYHHEWAQSIKAKHGTISTPSDAELILQQELGLKFAKVLEDAGVF 478

Query: 480 KLNEEGLEGFKRFTNSLN 497
           K        F RF  +LN
Sbjct: 479 KEK----SAFDRFIRTLN 492


Lambda     K      H
   0.318    0.136    0.398 

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: 701
Number of extensions: 30
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: 498
Length of database: 493
Length adjustment: 34
Effective length of query: 464
Effective length of database: 459
Effective search space:   212976
Effective search space used:   212976
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 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_010531699.1 ON01_RS14025 (UDP-glucose--hexose-1-phosphate uridylyltransferase)
to HMM TIGR01239 (galT: galactose-1-phosphate uridylyltransferase (EC 2.7.7.12))

# 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/TIGR01239.hmm
# target sequence database:        /tmp/gapView.3731038.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01239  [M=489]
Accession:   TIGR01239
Description: galT_2: galactose-1-phosphate uridylyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.5e-206  672.4   5.3   2.9e-206  672.2   5.3    1.0  1  NCBI__GCF_000224785.1:WP_010531699.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000224785.1:WP_010531699.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  672.2   5.3  2.9e-206  2.9e-206       1     488 [.       5     490 ..       5     491 .. 0.97

  Alignments for each domain:
  == domain 1  score: 672.2 bits;  conditional E-value: 2.9e-206
                             TIGR01239   1 lveefieqalenkdieeldrlylrnkllellglesadeekkesekvnqssldlldqllkaaaenglleevkeq 73 
                                           +++ +i++a++ + ie++d++y+rn++++ l+l+  + + + s+    s +dlld+l++ a++  ++++v ++
  NCBI__GCF_000224785.1:WP_010531699.1   5 HINALIDKAIQSGLIEKQDHIYVRNQIMHYLKLDGDKGTGSMSHSD-ASIPDLLDELVAYAVRHHVIDDVFDD 76 
                                           699******************************9877777777665.79************************ PP

                             TIGR01239  74 kelleaklldlitPrPskvnrefwekykssPeqatkefyqlskrveyvktdaiakniaykaetkyGdleitin 146
                                           ke+l a+++++++ rPs++n  f+eky  sPe at++fyqlsk+ +y+++++i kni++ka+t+yGdl+itin
  NCBI__GCF_000224785.1:WP_010531699.1  77 KEILAANIMNCFVARPSVINAVFQEKYSKSPEAATDYFYQLSKDSNYIQMKRIEKNIHFKANTEYGDLDITIN 149
                                           ************************************************************************* PP

                             TIGR01239 147 lskPekdpkaiaaake.akassyPacqlcleneGflGsvnkparsnhrivrvsledeewgfqfsPyayfnehs 218
                                           lskPekdp +i + +e +k  +yP+c lc+eneG+ G++  par nhr+++v l +e+w++q+sPy+y+nehs
  NCBI__GCF_000224785.1:WP_010531699.1 150 LSKPEKDPEQIKREREnTKHIDYPKCVLCVENEGYAGRIGYPARANHRVIEVPLLGEKWYLQYSPYVYYNEHS 222
                                           ************998625789**************************************************** PP

                             TIGR01239 219 ivlkekhePmeiskktferllsflekfPhyfiGsnadlPivGGsilshdhyqgGrhdfPmekaelkekveled 291
                                           ivl ekh+ m+i+k+ ferll+f++kfPhyfiGsnadlPi+GGsilshdhyqgGr+ f m  ae+   +el++
  NCBI__GCF_000224785.1:WP_010531699.1 223 IVLAEKHRNMKIDKQGFERLLAFIDKFPHYFIGSNADLPIIGGSILSHDHYQGGRYRFAMTDAEEAFSFELDN 295
                                           ************************************************************************* PP

                             TIGR01239 292 ypdvsagivkwPmsvlrlksedkgelaeaadkilktwksysdekldikaksdgtphhtvtPiarrrddkyeld 364
                                           + +v a +++wP+sv+rl+  dk+el +aad++l+twk ysde++dika s++tph+t+tPiar r++ yeld
  NCBI__GCF_000224785.1:WP_010531699.1 296 HDNVTAQVLNWPLSVIRLNCSDKKELLDAADHVLQTWKHYSDESIDIKAFSGNTPHNTITPIARMRNGAYELD 368
                                           ************************************************************************* PP

                             TIGR01239 365 lvlrdnqtseeyPdGifhPhkdvhhikkeniGlievmGlailPgrlkkelkevekyllgqdnqlaeihkewad 437
                                           lvlr+n+tsee+P GifhPh+dvhhikkeniGlievmGla+lP+rlk+el e++++ll++  +++e h+ewa+
  NCBI__GCF_000224785.1:WP_010531699.1 369 LVLRNNRTSEEHPMGIFHPHSDVHHIKKENIGLIEVMGLAVLPPRLKDELAEIKEFLLDKPSNIEEYHHEWAQ 441
                                           ************************************************************************* PP

                             TIGR01239 438 klkeke.ni.tkenvkevvkeevgevfarvledaGvfkqtaeGkkafrkfidf 488
                                            +k+k+ +i t  +++ ++++e+g  fa+vledaGvfk++     af +fi +
  NCBI__GCF_000224785.1:WP_010531699.1 442 SIKAKHgTIsTPSDAELILQQELGLKFAKVLEDAGVFKEK----SAFDRFIRT 490
                                           *****98663568999**********************85....578888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (489 nodes)
Target sequences:                          1  (493 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: 27.61
//
[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 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