GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylA in Caldicellulosiruptor hydrothermalis 108

Align xylose isomerase (EC 5.3.1.5) (characterized)
to candidate WP_013403911.1 CALHY_RS10405 xylose isomerase

Query= BRENDA::D2DK62
         (438 letters)



>NCBI__GCF_000166355.1:WP_013403911.1
          Length = 438

 Score =  798 bits (2061), Expect = 0.0
 Identities = 377/438 (86%), Positives = 416/438 (94%)

Query: 1   MEYFKNVPQIKYEGPKSNNPYAFKFYNPDEIIDGKPLKEHLRFSVAYWHTFTANGTDPFG 60
           M+YFK++P +KYEGP+S+NP+AFK+YNPDEIIDGKPLK+HLRF+VAYWHTF A G DPFG
Sbjct: 1   MKYFKDIPGVKYEGPQSDNPFAFKYYNPDEIIDGKPLKDHLRFAVAYWHTFCATGADPFG 60

Query: 61  APTMQRPWNHLSDPMDIAKARVEAAFEFFEKLDVPFFCFHDRDIAPEGENLRETNKNLDT 120
            PT+ RPW+  S+PMD AKARVEAAFEFFEKL+VPFFCFHDRDIAPEGENLRETNKNLD 
Sbjct: 61  QPTIVRPWDRFSNPMDNAKARVEAAFEFFEKLNVPFFCFHDRDIAPEGENLRETNKNLDE 120

Query: 121 IVAMIKDYLKTSKTKVLWGTANLFSNPRFVHGAATSCNADVFAYAAAQVKKALEITKELG 180
           IV+MIK+YLKTSKTKVLWGTANLFS+PR+VHGAATSCNADVFAYAAAQVKKALE+TKELG
Sbjct: 121 IVSMIKEYLKTSKTKVLWGTANLFSHPRYVHGAATSCNADVFAYAAAQVKKALEVTKELG 180

Query: 181 GQNYVFWGGREGYETLLNTDMELELDNLARFLHMAVEYAKEIGFEGQLLIEPKPKEPTKH 240
           G+NYVFWGGREGYETLLNTDMELELDNLARFL MAV+YAKEIGF+GQ LIEPKPKEPTKH
Sbjct: 181 GENYVFWGGREGYETLLNTDMELELDNLARFLRMAVDYAKEIGFDGQFLIEPKPKEPTKH 240

Query: 241 QYDFDAANVYAFLKKYDLDKYFKLNIEANHATLAGHDFQHELRYARINNMLGSIDANMGD 300
           QYDFDAA+VY FLKKYDLDKYFKLNIE NHATLAGHDF HELR+ARINNMLGSIDANMGD
Sbjct: 241 QYDFDAAHVYGFLKKYDLDKYFKLNIEVNHATLAGHDFHHELRFARINNMLGSIDANMGD 300

Query: 301 MLLGWDTDQFPTDIRMTTLAMYEVIKMGGFDKGGLNFDAKVRRASFEPEDLFLGHIAGMD 360
           +LLGWDTDQFPTD+R+TTLAMYEVIKMGGFDKGGLNFDAKVRR SFE EDL +GHIAGMD
Sbjct: 301 LLLGWDTDQFPTDVRLTTLAMYEVIKMGGFDKGGLNFDAKVRRGSFELEDLVIGHIAGMD 360

Query: 361 AFAKGFKVAYKLVKDGVFDRFIEERYKSYREGIGAEIVSGKANFKTLEEYALNNPKIENK 420
           AFAKGFK+AYKLVK+GVFD+FI+ERYKSY+EGIGA+IVSG+ANFK LEEYAL+  KIENK
Sbjct: 361 AFAKGFKIAYKLVKNGVFDKFIDERYKSYKEGIGAKIVSGEANFKMLEEYALSLDKIENK 420

Query: 421 SGKQELLESILNQYLFSE 438
           SGKQELLE ILN+Y+F+E
Sbjct: 421 SGKQELLEMILNKYMFTE 438


Lambda     K      H
   0.320    0.137    0.413 

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: 830
Number of extensions: 27
Number of successful extensions: 1
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: 438
Length of database: 438
Length adjustment: 32
Effective length of query: 406
Effective length of database: 406
Effective search space:   164836
Effective search space used:   164836
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: 51 (24.3 bits)

Align candidate WP_013403911.1 CALHY_RS10405 (xylose isomerase)
to HMM TIGR02630 (xylA: xylose isomerase (EC 5.3.1.5))

# 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/TIGR02630.hmm
# target sequence database:        /tmp/gapView.2530906.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02630  [M=435]
Accession:   TIGR02630
Description: xylose_isom_A: xylose isomerase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.2e-230  751.7   2.7   1.4e-230  751.6   2.7    1.0  1  NCBI__GCF_000166355.1:WP_013403911.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000166355.1:WP_013403911.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  751.6   2.7  1.4e-230  1.4e-230       1     435 []       3     435 ..       3     435 .. 0.99

  Alignments for each domain:
  == domain 1  score: 751.6 bits;  conditional E-value: 1.4e-230
                             TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltda 73 
                                           +f++i  vkyeG++s+np+afkyynp+e+i+gk +kdhlrfavayWht++a+gaDpfG+ t+ rpwd + +++
  NCBI__GCF_000166355.1:WP_013403911.1   3 YFKDIPGVKYEGPQSDNPFAFKYYNPDEIIDGKPLKDHLRFAVAYWHTFCATGADPFGQPTIVRPWD-RFSNP 74 
                                           8*****************************************************************9.68*** PP

                             TIGR02630  74 ldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshp 146
                                           +d+aka+v+aafe++ekl+v+++cfhD+Diapeg++l+etn+nldeiv+++ke+ k+++ k+LWgtanlfshp
  NCBI__GCF_000166355.1:WP_013403911.1  75 MDNAKARVEAAFEFFEKLNVPFFCFHDRDIAPEGENLRETNKNLDEIVSMIKEYLKTSKTKVLWGTANLFSHP 147
                                           ************************************************************************* PP

                             TIGR02630 147 ryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyak 219
                                           ryv+Gaats++advfayaaaqvkkalevtk+lggenyvfWGGreGyetLlntd++leldnlarfl++avdyak
  NCBI__GCF_000166355.1:WP_013403911.1 148 RYVHGAATSCNADVFAYAAAQVKKALEVTKELGGENYVFWGGREGYETLLNTDMELELDNLARFLRMAVDYAK 220
                                           ************************************************************************* PP

                             TIGR02630 220 kigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGs 292
                                           +igf+gq+liePkPkePtkhqyDfDaa v++flkkydLdk+fklnie+nhatLagh f+helr ar +++lGs
  NCBI__GCF_000166355.1:WP_013403911.1 221 EIGFDGQFLIEPKPKEPTKHQYDFDAAHVYGFLKKYDLDKYFKLNIEVNHATLAGHDFHHELRFARINNMLGS 293
                                           ************************************************************************* PP

                             TIGR02630 293 iDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafargl 365
                                           iDan gdlllGWDtD+fptdv  +tlamyev+k gg++kGGlnfdakvrr s++ eDl+++hiagmDafa+g+
  NCBI__GCF_000166355.1:WP_013403911.1 294 IDANMGDLLLGWDTDQFPTDVRLTTLAMYEVIKMGGFDKGGLNFDAKVRRGSFELEDLVIGHIAGMDAFAKGF 366
                                           ************************************************************************* PP

                             TIGR02630 366 kvaaklledgaleklveeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                           k+a+kl+++g+++k+++ery+s++++iG++i++g+a+++ le+yal+ ++ +e+ksg+qelle+++nky+
  NCBI__GCF_000166355.1:WP_013403911.1 367 KIAYKLVKNGVFDKFIDERYKSYKEGIGAKIVSGEANFKMLEEYALSLDK-IENKSGKQELLEMILNKYM 435
                                           ************************************************87.*****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (438 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: 14.39
//
[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:

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