Alignments for a candidate for xylA in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Pedobacter sp. GW460-11-11-14-LB5

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate CA265_RS19715 CA265_RS19715 xylose isomerase

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



>FitnessBrowser__Pedo557:CA265_RS19715
          Length = 443

 Score =  660 bits (1702), Expect = 0.0
 Identities = 315/433 (72%), Positives = 363/433 (83%)

Query: 5   YFPGIEKIKYEGRDSKNPFAFKFYDENKVVAGKTMKEHFKFAIAYWHSFNATGDDPFGPG 64
           +F GIE+IK+EG  S NP AF++YD NKVVAGKTM EHFKFA AYWHSFN  G DPFG  
Sbjct: 11  FFKGIEQIKFEGLGSDNPLAFRWYDANKVVAGKTMNEHFKFACAYWHSFNGNGADPFGGA 70

Query: 65  TKTFVWDQAEDALQRAKDKMDAAFEFITKIGAPYYCFHDVDLIDEGSTIEEYESRMKAIT 124
           T  F WD+ +DA++RAKDKMDAAFEFITK+  PYYCFHDVD++D    I E E R++A+ 
Sbjct: 71  THIFPWDEKKDAVERAKDKMDAAFEFITKMQIPYYCFHDVDVVDYSDDIAENERRLQALV 130

Query: 125 EYAKQKQVETGVKLLWGTANVFSNPRYMNGASTNPDFDVVSWAATQVKNSIDATIALGGE 184
           EYAKQKQ ++GVKLLWGTAN+FS+ RYMNGASTNPDF V++  A QVK ++DATIALGGE
Sbjct: 131 EYAKQKQADSGVKLLWGTANLFSHRRYMNGASTNPDFHVLAHGAAQVKAALDATIALGGE 190

Query: 185 NYVFWGGREGYMSLLNTDMKRETEHLAKFLTMARDYGRKQGFKGNFLIEPKPMEPTKHQY 244
           NYVFWGGREGYMSLLNT+MKRE EHLAKFL  A+DY RKQGFKG F IEPKP EP+KHQY
Sbjct: 191 NYVFWGGREGYMSLLNTNMKREQEHLAKFLHTAKDYARKQGFKGTFFIEPKPCEPSKHQY 250

Query: 245 DYDSATVVGFLRHYGLDKDFKLNIEVNHATLAGHTFQHELQVAADAGLLGSIDANRGDYQ 304
           DYD+ATV GFL+ Y L  DFKLN+EVNHATLAGHTFQHELQVA D GLLGSIDANRGDYQ
Sbjct: 251 DYDAATVKGFLQQYDLLADFKLNLEVNHATLAGHTFQHELQVAVDNGLLGSIDANRGDYQ 310

Query: 305 NGWDTDQFALNLQELTESLLVILEAGGLQGGGVNFDAKLRRNSTDLDDLFHAHIGSMDAF 364
           NGWDTDQF  ++ ELTE++L+ILE GGLQGGGVNFDAK+RRNSTD  DLF+AHIG MD F
Sbjct: 311 NGWDTDQFPNDINELTETMLIILEGGGLQGGGVNFDAKIRRNSTDPKDLFYAHIGGMDIF 370

Query: 365 ARALLIANDILEQSEYKALRKKRYASFDGGKGKEFEEGKLTLEDLREHAIATGEPASTSG 424
           ARAL+ A+ IL++S+YK +R +RYASFD GKG EFE+GKL+LEDLR +A   GEPA  SG
Sbjct: 371 ARALITADAILQKSDYKKIRTERYASFDSGKGAEFEQGKLSLEDLRNYAAENGEPAVLSG 430

Query: 425 KQEMYENIINQYI 437
           KQE  EN+IN+YI
Sbjct: 431 KQEYLENLINRYI 443


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: 692
Number of extensions: 19
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: 443
Length adjustment: 32
Effective length of query: 405
Effective length of database: 411
Effective search space:   166455
Effective search space used:   166455
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 CA265_RS19715 CA265_RS19715 (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.12832.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   5.3e-207  673.9   6.3   5.9e-207  673.7   6.3    1.0  1  lcl|FitnessBrowser__Pedo557:CA265_RS19715  CA265_RS19715 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Pedo557:CA265_RS19715  CA265_RS19715 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  673.7   6.3  5.9e-207  5.9e-207       1     435 []      11     443 .]      11     443 .] 0.99

  Alignments for each domain:
  == domain 1  score: 673.7 bits;  conditional E-value: 5.9e-207
                                  TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdk 68 
                                                ff++ie++k+eG  s+nplaf++y++++v++gk+m++h++fa ayWh+++ +gaDpfG++t  +pwd+
  lcl|FitnessBrowser__Pedo557:CA265_RS19715  11 FFKGIEQIKFEGLGSDNPLAFRWYDANKVVAGKTMNEHFKFACAYWHSFNGNGADPFGGATHIFPWDE 78 
                                                8******************************************************************5 PP

                                  TIGR02630  69 eltdaldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklL 136
                                                 ++da+++ak+k+daafe+++k++++yycfhDvD+++ +++++e+++ l+++v+++k+kq+++gvklL
  lcl|FitnessBrowser__Pedo557:CA265_RS19715  79 -KKDAVERAKDKMDAAFEFITKMQIPYYCFHDVDVVDYSDDIAENERRLQALVEYAKQKQADSGVKLL 145
                                                .6****************************************************************** PP

                                  TIGR02630 137 WgtanlfshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlklel 204
                                                Wgtanlfsh+ry++Ga+t+pd++v+a++aaqvk+al++t  lggenyvfWGGreGy++Llnt++k+e+
  lcl|FitnessBrowser__Pedo557:CA265_RS19715 146 WGTANLFSHRRYMNGASTNPDFHVLAHGAAQVKAALDATIALGGENYVFWGGREGYMSLLNTNMKREQ 213
                                                ******************************************************************** PP

                                  TIGR02630 205 dnlarflklavdyakkigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatL 272
                                                ++la+fl+ a+dya+k gfkg+++iePkP eP+khqyD+Daatv +fl++ydL  dfkln+e+nhatL
  lcl|FitnessBrowser__Pedo557:CA265_RS19715 214 EHLAKFLHTAKDYARKQGFKGTFFIEPKPCEPSKHQYDYDAATVKGFLQQYDLLADFKLNLEVNHATL 281
                                                ******************************************************************** PP

                                  TIGR02630 273 aghtfehelrvarelgllGsiDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakv 340
                                                aghtf+hel+va ++gllGsiDanrgd+++GWDtD+fp+d+ e+t +m+ +l+ ggl+ GG+nfdak+
  lcl|FitnessBrowser__Pedo557:CA265_RS19715 282 AGHTFQHELQVAVDNGLLGSIDANRGDYQNGWDTDQFPNDINELTETMLIILEGGGLQGGGVNFDAKI 349
                                                ******************************************************************** PP

                                  TIGR02630 341 rresldaeDlllahiagmDafarglkvaaklledgaleklveeryesfdseiGkeieegkadleelek 408
                                                rr+s+d++Dl++ahi+gmD far+l +a ++l+++ ++k+  ery+sfds+ G+e+e+gk +le+l +
  lcl|FitnessBrowser__Pedo557:CA265_RS19715 350 RRNSTDPKDLFYAHIGGMDIFARALITADAILQKSDYKKIRTERYASFDSGKGAEFEQGKLSLEDLRN 417
                                                ******************************************************************** PP

                                  TIGR02630 409 yalekeeeaekksgrqelleslinkyl 435
                                                ya+e++e ++  sg+qe+le+lin+y+
  lcl|FitnessBrowser__Pedo557:CA265_RS19715 418 YAAENGE-PAVLSGKQEYLENLINRYI 443
                                                *****97.*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (443 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.10
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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