GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galE in Frischella perrara PEB0191

Align UDP-glucose 4-epimerase (EC 5.1.3.2) (characterized)
to candidate WP_039104092.1 FPB0191_RS03585 UDP-glucose 4-epimerase GalE

Query= BRENDA::P09147
         (338 letters)



>NCBI__GCF_000807275.1:WP_039104092.1
          Length = 338

 Score =  439 bits (1129), Expect = e-128
 Identities = 210/338 (62%), Positives = 263/338 (77%), Gaps = 1/338 (0%)

Query: 1   MRVLVTGGSGYIGSHTCVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKHPTFVEGDIR 60
           M +LVTGG GYIGSHTCV+LL++G+  II+DNL NSK+SVL  IE++ GK P F  GD+ 
Sbjct: 1   MNILVTGGLGYIGSHTCVKLLESGYTPIIVDNLYNSKKSVLYRIEQITGKKPLFYYGDVC 60

Query: 61  NEALMTEILHDHAIDTVIHFAGLKAVGESVQKPLEYYDNNVNGTLRLISAMRAANVKNFI 120
           +   +  +  ++ I  VIHFAGLKAVGESV KPL YY+NNV+G++ L   M+   V N I
Sbjct: 61  DRTFLNTVFEENNIAGVIHFAGLKAVGESVTKPLTYYENNVHGSIVLAQVMQEHQVYNLI 120

Query: 121 FSSSATVYGDQPKIPYVESFPTGTPQSPYGKSKLMVEQILTDLQKAQPDWSIALLRYFNP 180
           FSSSATVYGD+  +PYVESF TG+  +PYG SK MVE+I  DL K    WSI+LLRYFNP
Sbjct: 121 FSSSATVYGDKNPVPYVESFETGSITNPYGWSKYMVERIYQDLAKTSSKWSISLLRYFNP 180

Query: 181 VGAHPSGDMGEDPQGIPNNLMPYIAQVAVGRRDSLAIFGNDYPTEDGTGVRDYIHVMDLA 240
           VGAH SG +GEDPQGIPNNLMPYIAQVA+G+R+ L+I+GNDYPT+DGTGVRDYIHV DLA
Sbjct: 181 VGAHASGLIGEDPQGIPNNLMPYIAQVAIGKREKLSIYGNDYPTKDGTGVRDYIHVEDLA 240

Query: 241 DGHVVAMEKLANKPGVHIYNLGAGVGNSVLDVVNAFSKACGKPVNYHFAPRREGDLPAYW 300
            GHV A+ K  N+ GVHIYNLGAG+G+SV DV+ A+  ACGK + Y    RR GD+ A+W
Sbjct: 241 IGHVAAL-KTMNESGVHIYNLGAGIGSSVFDVLGAYENACGKKLAYQIVGRRAGDIAAFW 299

Query: 301 ADASKADRELNWRVTRTLDEMAQDTWHWQSRHPQGYPD 338
           ADASKA++ELNWR    L++MA+D+W+WQ+++P GYP+
Sbjct: 300 ADASKAEKELNWRTKYNLNDMAKDSWNWQTKNPNGYPE 337


Lambda     K      H
   0.318    0.136    0.419 

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: 437
Number of extensions: 15
Number of successful extensions: 2
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: 338
Length of database: 338
Length adjustment: 28
Effective length of query: 310
Effective length of database: 310
Effective search space:    96100
Effective search space used:    96100
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: 49 (23.5 bits)

Align candidate WP_039104092.1 FPB0191_RS03585 (UDP-glucose 4-epimerase GalE)
to HMM TIGR01179 (galE: UDP-glucose 4-epimerase GalE (EC 5.1.3.2))

# 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/TIGR01179.hmm
# target sequence database:        /tmp/gapView.2798844.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01179  [M=332]
Accession:   TIGR01179
Description: galE: UDP-glucose 4-epimerase GalE
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-137  442.4   0.2   4.6e-137  442.2   0.2    1.0  1  NCBI__GCF_000807275.1:WP_039104092.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000807275.1:WP_039104092.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.2   0.2  4.6e-137  4.6e-137       1     331 [.       2     334 ..       2     335 .. 0.99

  Alignments for each domain:
  == domain 1  score: 442.2 bits;  conditional E-value: 4.6e-137
                             TIGR01179   1 kiLvtGgaGyiGshvvrqllekgkevvvlDnlskgskealkalekit..evklvegdladkekleavleeeki 71 
                                           +iLvtGg GyiGsh++++lle+g+  +++Dnl +++k++l ++e+it  +  ++ gd+ d++ l++v+ee++i
  NCBI__GCF_000807275.1:WP_039104092.1   2 NILVTGGLGYIGSHTCVKLLESGYTPIIVDNLYNSKKSVLYRIEQITgkKPLFYYGDVCDRTFLNTVFEENNI 74 
                                           59********************************************998999********************* PP

                             TIGR01179  72 daviHfaaliavgEsvkePlkYYennvvntleLleamqkagvkkliFsssaavYgesekvpisEespln.pin 143
                                             viHfa+l+avgEsv++Pl YYennv+++++L ++mq+++v +liFsssa+vYg+++ vp+ E+++++  +n
  NCBI__GCF_000807275.1:WP_039104092.1  75 AGVIHFAGLKAVGESVTKPLTYYENNVHGSIVLAQVMQEHQVYNLIFSSSATVYGDKNPVPYVESFETGsITN 147
                                           ********************************************************************9789* PP

                             TIGR01179 144 pYGrsklmvErilkdlkkadkelkvviLRYFnvaGAdeegeiGeasknat.hliklvaevavgkrekleifGt 215
                                           pYG sk mvEri +dl+k+ +++++ +LRYFn++GA+ +g iGe++++++ +l++++a+va+gkrekl+i+G+
  NCBI__GCF_000807275.1:WP_039104092.1 148 PYGWSKYMVERIYQDLAKTSSKWSISLLRYFNPVGAHASGLIGEDPQGIPnNLMPYIAQVAIGKREKLSIYGN 220
                                           **************************************************9********************** PP

                             TIGR01179 216 dyptkDGtcvRDyiHveDlaeaHlaalealeeggesevynlGagqgfsvkevieavkkvsgkdikveladrRa 288
                                           dyptkDGt+vRDyiHveDla +H+aal++++e +++++ynlGag g sv +v+ a ++++gk++++++  rRa
  NCBI__GCF_000807275.1:WP_039104092.1 221 DYPTKDGTGVRDYIHVEDLAIGHVAALKTMNE-SGVHIYNLGAGIGSSVFDVLGAYENACGKKLAYQIVGRRA 292
                                           ****************************9986.89************************************** PP

                             TIGR01179 289 GDpaslvadaskikrelgwkpkyddLeeiiksawdWekklkeg 331
                                           GD+a+++adask+++el+w++ky+ L+++ k++w+W++k+++g
  NCBI__GCF_000807275.1:WP_039104092.1 293 GDIAAFWADASKAEKELNWRTKYN-LNDMAKDSWNWQTKNPNG 334
                                           ************************.**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (332 nodes)
Target sequences:                          1  (338 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: 27.05
//
[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