Alignments for a candidate for xylA in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate Echvi_1876 Echvi_1876 xylose isomerase

Query= reanno::Cola:Echvi_1876
         (437 letters)



>FitnessBrowser__Cola:Echvi_1876
          Length = 437

 Score =  894 bits (2310), Expect = 0.0
 Identities = 437/437 (100%), Positives = 437/437 (100%)

Query: 1   MSKTYFPGIEKIKYEGRDSKNPFAFKFYDENKVVAGKTMKEHFKFAIAYWHSFNATGDDP 60
           MSKTYFPGIEKIKYEGRDSKNPFAFKFYDENKVVAGKTMKEHFKFAIAYWHSFNATGDDP
Sbjct: 1   MSKTYFPGIEKIKYEGRDSKNPFAFKFYDENKVVAGKTMKEHFKFAIAYWHSFNATGDDP 60

Query: 61  FGPGTKTFVWDQAEDALQRAKDKMDAAFEFITKIGAPYYCFHDVDLIDEGSTIEEYESRM 120
           FGPGTKTFVWDQAEDALQRAKDKMDAAFEFITKIGAPYYCFHDVDLIDEGSTIEEYESRM
Sbjct: 61  FGPGTKTFVWDQAEDALQRAKDKMDAAFEFITKIGAPYYCFHDVDLIDEGSTIEEYESRM 120

Query: 121 KAITEYAKQKQVETGVKLLWGTANVFSNPRYMNGASTNPDFDVVSWAATQVKNSIDATIA 180
           KAITEYAKQKQVETGVKLLWGTANVFSNPRYMNGASTNPDFDVVSWAATQVKNSIDATIA
Sbjct: 121 KAITEYAKQKQVETGVKLLWGTANVFSNPRYMNGASTNPDFDVVSWAATQVKNSIDATIA 180

Query: 181 LGGENYVFWGGREGYMSLLNTDMKRETEHLAKFLTMARDYGRKQGFKGNFLIEPKPMEPT 240
           LGGENYVFWGGREGYMSLLNTDMKRETEHLAKFLTMARDYGRKQGFKGNFLIEPKPMEPT
Sbjct: 181 LGGENYVFWGGREGYMSLLNTDMKRETEHLAKFLTMARDYGRKQGFKGNFLIEPKPMEPT 240

Query: 241 KHQYDYDSATVVGFLRHYGLDKDFKLNIEVNHATLAGHTFQHELQVAADAGLLGSIDANR 300
           KHQYDYDSATVVGFLRHYGLDKDFKLNIEVNHATLAGHTFQHELQVAADAGLLGSIDANR
Sbjct: 241 KHQYDYDSATVVGFLRHYGLDKDFKLNIEVNHATLAGHTFQHELQVAADAGLLGSIDANR 300

Query: 301 GDYQNGWDTDQFALNLQELTESLLVILEAGGLQGGGVNFDAKLRRNSTDLDDLFHAHIGS 360
           GDYQNGWDTDQFALNLQELTESLLVILEAGGLQGGGVNFDAKLRRNSTDLDDLFHAHIGS
Sbjct: 301 GDYQNGWDTDQFALNLQELTESLLVILEAGGLQGGGVNFDAKLRRNSTDLDDLFHAHIGS 360

Query: 361 MDAFARALLIANDILEQSEYKALRKKRYASFDGGKGKEFEEGKLTLEDLREHAIATGEPA 420
           MDAFARALLIANDILEQSEYKALRKKRYASFDGGKGKEFEEGKLTLEDLREHAIATGEPA
Sbjct: 361 MDAFARALLIANDILEQSEYKALRKKRYASFDGGKGKEFEEGKLTLEDLREHAIATGEPA 420

Query: 421 STSGKQEMYENIINQYI 437
           STSGKQEMYENIINQYI
Sbjct: 421 STSGKQEMYENIINQYI 437


Lambda     K      H
   0.317    0.135    0.400 

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: 847
Number of extensions: 22
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: 437
Length of database: 437
Length adjustment: 32
Effective length of query: 405
Effective length of database: 405
Effective search space:   164025
Effective search space used:   164025
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate Echvi_1876 Echvi_1876 (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.27787.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-210  685.8   6.8   1.4e-210  685.6   6.8    1.0  1  lcl|FitnessBrowser__Cola:Echvi_1876  Echvi_1876 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_1876  Echvi_1876 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.6   6.8  1.4e-210  1.4e-210       1     435 []       5     437 .]       5     437 .] 0.99

  Alignments for each domain:
  == domain 1  score: 685.6 bits;  conditional E-value: 1.4e-210
                            TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltdal 74 
                                          +f++iek+kyeG+dsknp+afk+y++++v++gk+mk+h++fa+ayWh+++a+g DpfG gt+++ wd+  +dal
  lcl|FitnessBrowser__Cola:Echvi_1876   5 YFPGIEKIKYEGRDSKNPFAFKFYDENKVVAGKTMKEHFKFAIAYWHSFNATGDDPFGPGTKTFVWDQ-AEDAL 77 
                                          8******************************************************************6.6**** PP

                            TIGR02630  75 dkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshpry 148
                                          ++ak+k+daafe+++k+g++yycfhDvD+ +eg++++e+++ +++i++++k+kq etgvklLWgtan+fs+pry
  lcl|FitnessBrowser__Cola:Echvi_1876  78 QRAKDKMDAAFEFITKIGAPYYCFHDVDLIDEGSTIEEYESRMKAITEYAKQKQVETGVKLLWGTANVFSNPRY 151
                                          ************************************************************************** PP

                            TIGR02630 149 vaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyakkig 222
                                          ++Ga+t+pd+dv+++aa+qvk+++++t  lggenyvfWGGreGy++Llntd+k+e+++la+fl++a+dy +k g
  lcl|FitnessBrowser__Cola:Echvi_1876 152 MNGASTNPDFDVVSWAATQVKNSIDATIALGGENYVFWGGREGYMSLLNTDMKRETEHLAKFLTMARDYGRKQG 225
                                          ************************************************************************** PP

                            TIGR02630 223 fkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGsiDan 296
                                          fkg++liePkP+ePtkhqyD+D+atv++fl++y+Ldkdfklnie+nhatLaghtf+hel+va+++gllGsiDan
  lcl|FitnessBrowser__Cola:Echvi_1876 226 FKGNFLIEPKPMEPTKHQYDYDSATVVGFLRHYGLDKDFKLNIEVNHATLAGHTFQHELQVAADAGLLGSIDAN 299
                                          ************************************************************************** PP

                            TIGR02630 297 rgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafarglkvaak 370
                                          rgd+++GWDtD+f+ +++e+t  ++ +l+aggl+ GG+nfdak+rr+s+d +Dl++ahi++mDafar+l +a++
  lcl|FitnessBrowser__Cola:Echvi_1876 300 RGDYQNGWDTDQFALNLQELTESLLVILEAGGLQGGGVNFDAKLRRNSTDLDDLFHAHIGSMDAFARALLIAND 373
                                          ************************************************************************** PP

                            TIGR02630 371 lledgaleklveeryesfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                          +le++++++l ++ry+sfd + Gke+eegk +le+l ++a+ ++e ++++sg+qe++e++in+y+
  lcl|FitnessBrowser__Cola:Echvi_1876 374 ILEQSEYKALRKKRYASFDGGKGKEFEEGKLTLEDLREHAIATGE-PASTSGKQEMYENIINQYI 437
                                          *******************************************97.*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (437 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 10.96
//
[ok]

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

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Protein sequences (fasta format)
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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