GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galT in Gracilibacillus halophilus YIM-C55.5

Align Galactose-1-phosphate uridylyltransferase; Gal-1-P uridylyltransferase; EC 2.7.7.12; UDP-glucose--hexose-1-phosphate uridylyltransferase (uncharacterized)
to candidate WP_003465239.1 J416_RS03825 UDP-glucose--hexose-1-phosphate uridylyltransferase

Query= curated2:Q9KDV2
         (508 letters)



>NCBI__GCF_000359605.1:WP_003465239.1
          Length = 499

 Score =  516 bits (1329), Expect = e-151
 Identities = 263/507 (51%), Positives = 352/507 (69%), Gaps = 12/507 (2%)

Query: 4   SSIAIQIEALLTYALQHGLITKWDIDASRNRVLDVLDLDE-LEPVEQVDVECEMPYPILE 62
           ++++  +E L+  A+   +IT+ D   +RN++L  L ++E +E      V  ++P  +LE
Sbjct: 2   TNLSQTVEVLVQRAIDKSMITRQDAIYARNQILSYLHVNEFIEEQSLAHVNDDIP-DLLE 60

Query: 63  NILDWAAENGRLEANTVTYRDLLDTKLMGALLGQPSETIRTFYERYEQQGPEEATKVFYD 122
           ++ D+AA +  +E + +  R+ L  ++M   + +PSE  RTFY++YE+  P  AT  FY 
Sbjct: 61  SLTDYAARHNIIE-DLLDEREKLSAQMMNVFVSKPSEINRTFYQKYEES-PVLATDFFYQ 118

Query: 123 FSKQVHYIRTDRIAKNEHWFSETPYGQLEITINLSKPEKDPKAIAQAKHL-QASSYPKCL 181
           FSK  +YI+T RIAKN  + + + YG L+ITINLSKPEKDP+ I + + L Q  +YP+CL
Sbjct: 119 FSKDTNYIQTKRIAKNIEFVTPSAYGDLDITINLSKPEKDPEQIKRERELKQEIAYPQCL 178

Query: 182 LCKENVGYRGRVNHPARQNLRVIPVELNQEQWYMQFSPYVYYNEHAIVFSGEHVPMKIST 241
           LCKEN GY GR+ HPAR N R+I + L  E W+ Q+SPYVYYNEH+IVFS EH PM I+ 
Sbjct: 179 LCKENEGYAGRIGHPARSNHRIIEIPLEGETWFFQYSPYVYYNEHSIVFSSEHRPMTITR 238

Query: 242 ETFARLLEFTEKFPHYFIGSNADLPIVGGSILSHDHFQGGNHAFPMAKASMEKTFSISRF 301
           +TF+RL  F E+FPHYFIGSNADLPIVGGSILSHDH+Q G + F M  A  E  FSI  F
Sbjct: 239 DTFSRLTAFVEQFPHYFIGSNADLPIVGGSILSHDHYQAGRYTFAMTNAEDEFRFSIDPF 298

Query: 302 PSVIAGIVKWPMSVVRLQGMDRSELVKAADHVYHAWQAYGDEAADIYPFTGDTPHNTITP 361
           PS+ A +VKWP+SV+RL+  DR  LV AA H+   W+ Y D  A+I  +T  TPHNTITP
Sbjct: 299 PSIEASVVKWPLSVIRLRHEDRHYLVNAAHHILTKWRDYSDPDANIVAYTEKTPHNTITP 358

Query: 362 IARRRGELFELDLVLRNNRTSKEHPDGIFHPHQEVHHIKKENIGLIEVMGLAVLPGRLKE 421
           IAR+RG  FELDLVLRNNRT+K+HP G+FHPH++VHHIKKENIGLIEVMGLAVLP RLK+
Sbjct: 359 IARKRGNQFELDLVLRNNRTTKQHPAGLFHPHEDVHHIKKENIGLIEVMGLAVLPPRLKD 418

Query: 422 ELELLAEALLSSDPRQVIARYEQIQKHEAWALAIKERHAHLHDSNVMDILRDEIGKVFAT 481
           ELE + +ALL  +    +A Y     H+ W  +IK+RH+ + +  V  I+  E+G+ FA 
Sbjct: 419 ELETIKQALLGEN--VTVADY-----HQNWVQSIKKRHSLITEETVTQIVEQELGEKFAR 471

Query: 482 ILAHAGVFKRTGEGAAAFDRFISTLNQ 508
           +L  AGV+KR   G  AF RFI T+N+
Sbjct: 472 VLEDAGVYKRDRAGRQAFQRFIDTVNE 498


Lambda     K      H
   0.319    0.135    0.404 

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: 683
Number of extensions: 32
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: 508
Length of database: 499
Length adjustment: 34
Effective length of query: 474
Effective length of database: 465
Effective search space:   220410
Effective search space used:   220410
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: 52 (24.6 bits)

Align candidate WP_003465239.1 J416_RS03825 (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.69168.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     2e-209  682.6   5.1   2.3e-209  682.4   5.1    1.0  1  NCBI__GCF_000359605.1:WP_003465239.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000359605.1:WP_003465239.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  682.4   5.1  2.3e-209  2.3e-209       2     489 .]       8     496 ..       7     496 .. 0.98

  Alignments for each domain:
  == domain 1  score: 682.4 bits;  conditional E-value: 2.3e-209
                             TIGR01239   2 veefieqalenkdieeldrlylrnkllellglesadeekkesekvnqssldlldqllkaaaenglleevkeqk 74 
                                           ve +++ a++++ i ++d +y rn++l  l +++  ee++   +vn+  +dll+ l + aa+ + +e++ +++
  NCBI__GCF_000359605.1:WP_003465239.1   8 VEVLVQRAIDKSMITRQDAIYARNQILSYLHVNEFIEEQSL-AHVNDDIPDLLESLTDYAARHNIIEDLLDER 79 
                                           7889*****************************99777665.567789************************* PP

                             TIGR01239  75 elleaklldlitPrPskvnrefwekykssPeqatkefyqlskrveyvktdaiakniaykaetkyGdleitinl 147
                                           e l+a+++++++ +Ps++nr f++ky+ sP  at+ fyq+sk+++y++t++iakni++ +++ yGdl+itinl
  NCBI__GCF_000359605.1:WP_003465239.1  80 EKLSAQMMNVFVSKPSEINRTFYQKYEESPVLATDFFYQFSKDTNYIQTKRIAKNIEFVTPSAYGDLDITINL 152
                                           ************************************************************************* PP

                             TIGR01239 148 skPekdpkaiaaakeakas.syPacqlcleneGflGsvnkparsnhrivrvsledeewgfqfsPyayfnehsi 219
                                           skPekdp +i + +e k+   yP+c+lc+eneG+ G++ +parsnhri+++ le+e w+fq+sPy+y+nehsi
  NCBI__GCF_000359605.1:WP_003465239.1 153 SKPEKDPEQIKRERELKQEiAYPQCLLCKENEGYAGRIGHPARSNHRIIEIPLEGETWFFQYSPYVYYNEHSI 225
                                           **************9987549**************************************************** PP

                             TIGR01239 220 vlkekhePmeiskktferllsflekfPhyfiGsnadlPivGGsilshdhyqgGrhdfPmekaelkekveledy 292
                                           v++++h+Pm i + tf+rl +f+e+fPhyfiGsnadlPivGGsilshdhyq+Gr++f m +ae + +++++ +
  NCBI__GCF_000359605.1:WP_003465239.1 226 VFSSEHRPMTITRDTFSRLTAFVEQFPHYFIGSNADLPIVGGSILSHDHYQAGRYTFAMTNAEDEFRFSIDPF 298
                                           ************************************************************************* PP

                             TIGR01239 293 pdvsagivkwPmsvlrlksedkgelaeaadkilktwksysdekldikaksdgtphhtvtPiarrrddkyeldl 365
                                           p ++a++vkwP+sv+rl+ ed++ l++aa +il +w+ ysd  ++i a+++ tph+t+tPiar+r++++eldl
  NCBI__GCF_000359605.1:WP_003465239.1 299 PSIEASVVKWPLSVIRLRHEDRHYLVNAAHHILTKWRDYSDPDANIVAYTEKTPHNTITPIARKRGNQFELDL 371
                                           ************************************************************************* PP

                             TIGR01239 366 vlrdnqtseeyPdGifhPhkdvhhikkeniGlievmGlailPgrlkkelkevekyllgqdnqlaeihkewadk 438
                                           vlr+n+t +++P G+fhPh+dvhhikkeniGlievmGla+lP+rlk+el  ++++llg++ ++a+ h++w + 
  NCBI__GCF_000359605.1:WP_003465239.1 372 VLRNNRTTKQHPAGLFHPHEDVHHIKKENIGLIEVMGLAVLPPRLKDELETIKQALLGENVTVADYHQNWVQS 444
                                           ************************************************************************* PP

                             TIGR01239 439 lkeke.nitkenvkevvkeevgevfarvledaGvfkqtaeGkkafrkfidfl 489
                                           +k+++  it+e+v+++v++e+ge farvledaGv+k    G++af++fid++
  NCBI__GCF_000359605.1:WP_003465239.1 445 IKKRHsLITEETVTQIVEQELGEKFARVLEDAGVYKRDRAGRQAFQRFIDTV 496
                                           *9998679******************************************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (489 nodes)
Target sequences:                          1  (499 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 19.84
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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