Alignments for a candidate for xylB in Beijerinckia indica ATCC 9039

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Beijerinckia indica ATCC 9039

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate WP_012382961.1 BIND_RS19310 xylulokinase

Query= reanno::Smeli:SMc03164
         (484 letters)



>NCBI__GCF_000019845.1:WP_012382961.1
          Length = 481

 Score =  546 bits (1407), Expect = e-160
 Identities = 270/478 (56%), Positives = 332/478 (69%), Gaps = 1/478 (0%)

Query: 1   MYLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLR 60
           M+LG+D+GTS VK++L+D ++RI+ +AS  L V RP PGWSEQDP  W+ A    +  L+
Sbjct: 1   MFLGIDIGTSAVKSVLVDADERILATASEPLQVSRPQPGWSEQDPDSWVSATLTTLDALK 60

Query: 61  ETHAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALD-GDPQFRAL 119
            +H  ALA V GIGLSGQMHGATLL   D  LRPCILWND RS  E   L    P+   +
Sbjct: 61  MSHGAALARVEGIGLSGQMHGATLLGPDDRPLRPCILWNDGRSTDECVTLTHAVPELSVI 120

Query: 120 TGNIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLD 179
           TGN+   GFTAPKL WVR++EP+IF R+  VLLPK Y+RL LTGE + EMSD+AGT WLD
Sbjct: 121 TGNLAMSGFTAPKLLWVRQHEPDIFRRIATVLLPKAYVRLALTGEKVDEMSDAAGTLWLD 180

Query: 180 TGKRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAAS 239
              R WS   LAAT L   QMP L+EG++ +G LR ELAAR+GM    VVAGGAGDNAA 
Sbjct: 181 VAARDWSNECLAATDLSRAQMPRLIEGSEPSGRLRSELAARYGMTTPPVVAGGAGDNAAG 240

Query: 240 ACGMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDA 299
           A G+G +  G AFVSLGTSG+++A    +  NP SAVHAFCHALP  WHQMGV+LSA   
Sbjct: 241 AVGLGAIRSGDAFVSLGTSGIVWATTNRFAANPSSAVHAFCHALPGLWHQMGVMLSAASC 300

Query: 300 LNWHSGVTGRSAAELTSELGESLKAPGSVTFLPYLSGERTPHNDATIRGVFAGLGHESSR 359
           L+W + + GRS A+L +EL      PG   F PYLSGERTPHNDA++RG FA L HE+ R
Sbjct: 301 LSWWARIVGRSEADLLAELPRRPSGPGVALFQPYLSGERTPHNDASLRGAFAELAHETDR 360

Query: 360 AVLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWLSSIATALNLPVDLPA 419
             LTQAVLEGV++ IRD L+AL  AGT+++  T IGGGSR+ +W++ +A  L LP+   A
Sbjct: 361 PALTQAVLEGVAYGIRDCLDALSQAGTRVESATVIGGGSRTHFWVALLADVLGLPLHRVA 420

Query: 420 DGDFGAAFGAARLGLIAATGADPAAVCTAPETAETIAPEASLVPAYEDAYQRYRRLYP 477
            G+ GAAFGAARLG +AATG  P AVC  P   ETI P  +    Y + Y+R+R LYP
Sbjct: 421 QGEVGAAFGAARLGRLAATGESPTAVCRPPAILETIVPTPAFTRTYAERYERWRNLYP 478


Lambda     K      H
   0.317    0.132    0.401 

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: 646
Number of extensions: 26
Number of successful extensions: 3
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: 484
Length of database: 481
Length adjustment: 34
Effective length of query: 450
Effective length of database: 447
Effective search space:   201150
Effective search space used:   201150
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: 52 (24.6 bits)

Align candidate WP_012382961.1 BIND_RS19310 (xylulokinase)
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

# 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/TIGR01312.hmm
# target sequence database:        /tmp/gapView.8332.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01312  [M=481]
Accession:   TIGR01312
Description: XylB: xylulokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-167  542.9   0.0   3.3e-167  542.8   0.0    1.0  1  lcl|NCBI__GCF_000019845.1:WP_012382961.1  BIND_RS19310 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000019845.1:WP_012382961.1  BIND_RS19310 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  542.8   0.0  3.3e-167  3.3e-167       1     480 [.       3     477 ..       3     478 .. 0.98

  Alignments for each domain:
  == domain 1  score: 542.8 bits;  conditional E-value: 3.3e-167
                                 TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeik 69 
                                               lGiD+gTs+vK +lvd+ ++++a++s++l+v++p+pgwsEqdp +w++a+ ++l++l+ ++    ++++
  lcl|NCBI__GCF_000019845.1:WP_012382961.1   3 LGIDIGTSAVKSVLVDADERILATASEPLQVSRPQPGWSEQDPDSWVSATLTTLDALKMSHGAALARVE 71 
                                               7******************************************************************** PP

                                 TIGR01312  70 aisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvr 138
                                               +i++sGQmHg++lL  ++++lrp+iLWnD r++ ec +l+++++  el  +tgnla+ gfTapKllWvr
  lcl|NCBI__GCF_000019845.1:WP_012382961.1  72 GIGLSGQMHGATLLGPDDRPLRPCILWNDGRSTDECVTLTHAVP--ELSVITGNLAMSGFTAPKLLWVR 138
                                               *******************************************9..9999******************* PP

                                 TIGR01312 139 khepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklves 207
                                               +hep++f+ria+vlLPk y+r+ Ltge+v e+sDA+GTl++dv+ r+ws+e l+a+dl+++++P+l+e+
  lcl|NCBI__GCF_000019845.1:WP_012382961.1 139 QHEPDIFRRIATVLLPKAYVRLALTGEKVDEMSDAAGTLWLDVAARDWSNECLAATDLSRAQMPRLIEG 207
                                               ********************************************************************* PP

                                 TIGR01312 208 sekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpega 276
                                               se +G++r+e+a+++G+ +   va+G+gdnaagA+Glg++++g+++vslGtSG+v+a++++  ++p++a
  lcl|NCBI__GCF_000019845.1:WP_012382961.1 208 SEPSGRLRSELAARYGMTTPPVVAGGAGDNAAGAVGLGAIRSGDAFVSLGTSGIVWATTNRFAANPSSA 276
                                               ********************************************************************* PP

                                 TIGR01312 277 vhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGERtPhld 345
                                               vh+Fchalpg w+++gv+lsa+s+l+w+++++g+++  +l++e  + + g    l++PylsGERtPh+d
  lcl|NCBI__GCF_000019845.1:WP_012382961.1 277 VHAFCHALPGLWHQMGVMLSAASCLSWWARIVGRSEA-DLLAELPRRPSGPGVALFQPYLSGERTPHND 344
                                               *********************************6665.78888889999988899************** PP

                                 TIGR01312 346 pqargsliGltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladil 414
                                               ++ rg ++ l+++t r  l++Avlegva+++rd ld+l + +g+++++ ++iGGG++ ++w  +lad+l
  lcl|NCBI__GCF_000019845.1:WP_012382961.1 345 ASLRGAFAELAHETDRPALTQAVLEGVAYGIRDCLDALSQ-AGTRVESATVIGGGSRTHFWVALLADVL 412
                                               ****************************************.67************************** PP

                                 TIGR01312 415 glevvvpe.eeegaalGaAilAaialgekdlveecseavvkqkesvepiaenveayeelyerykkly 480
                                               gl+++  +  e gaa+GaA+l+ +a++ ++ +++c+   + ++    p+ + +++y+e+yer+++ly
  lcl|NCBI__GCF_000019845.1:WP_012382961.1 413 GLPLHRVAqGEVGAAFGAARLGRLAATGESPTAVCRPPAILETIV--PTPAFTRTYAERYERWRNLY 477
                                               ****87665999***************999*********999998..88899999*********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (481 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 9.33
//
[ok]

This GapMind analysis is from Sep 24 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