Alignments for a candidate for xylB in Rhodococcus qingshengii djl-6-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Rhodococcus qingshengii djl-6-2

Align Xylulose kinase; Xylulokinase; EC 2.7.1.17 (uncharacterized)
to candidate WP_050654666.1 C1M55_RS22535 xylulokinase

Query= curated2:P12867
         (466 letters)



>NCBI__GCF_002893965.1:WP_050654666.1
          Length = 465

 Score =  577 bits (1488), Expect = e-169
 Identities = 286/457 (62%), Positives = 339/457 (74%), Gaps = 1/457 (0%)

Query: 1   MALVAGIDSSTQSCKVVIRDAETGALVRQGRASHPDGTEVHPDAWWSALQSAIEEAGGLD 60
           MALVAGIDSSTQSCKV++RDA++G LVR+GRA+HP GTE+ P  W  A+ SAI  AGGL 
Sbjct: 1   MALVAGIDSSTQSCKVIVRDADSGELVREGRAAHPVGTEIDPACWLEAMDSAIAAAGGLG 60

Query: 61  DVAAASVAGQQHGMVALDENGEVVRPALLWNDTRSAGAAADLIAELGGGEKWAEAVGIVP 120
           DVAA SV  QQHGMV LD  GEVVRPALLWNDTRSA AA DL+ ELGG + WA+AVG+VP
Sbjct: 61  DVAAVSVGAQQHGMVCLDSGGEVVRPALLWNDTRSAKAATDLVEELGGPKAWADAVGVVP 120

Query: 121 VASFTLTKLRWLARNEPANAAKVAAVCLPHDWLTWKLSGSTDIADIKTDRSDASGTLYWS 180
           VA+ T +KLRWLA +EP NA + AAVCLPHDWL+WKL GS  I ++ TD  DASGT Y++
Sbjct: 121 VAAVTASKLRWLADHEPGNADRTAAVCLPHDWLSWKLGGSGSIEELATDAGDASGTGYYA 180

Query: 181 AKTNEYRRDLLELGF-GRDLVLPEVLGPTGIAGHLPNGAPLGPGAGDNAAAALGTGALPG 239
           A T EYR+DLL L F GR   +P V  P    G   +G  +GPG GDNAAAALG GA+PG
Sbjct: 181 ASTREYRKDLLALAFRGRTPHVPRVASPNEKIGSTRSGGIVGPGTGDNAAAALGLGAVPG 240

Query: 240 DVIVSIGTSGTVFVSSDVAPVDGRGTVAGFADTTGRFLPIVVTLNAARVLDAAAKLLGVD 299
           DVI+SIGTSG V   S     D  G VAGFAD TG  LP+V TLN AR+LDA A +LGVD
Sbjct: 241 DVIISIGTSGVVSAVSATPTHDPGGNVAGFADATGLHLPLVCTLNGARILDATASILGVD 300

Query: 300 HDELSRLALSAPAGADGMVLVPYLEGERTPNRPDATGAIHGLTLKTSDPAHLARAAVEGM 359
           H ELSRLA +AP G DG+V++PY EGERTPNRPDATGA+HG  L+ S PAH ARAA+EG+
Sbjct: 301 HAELSRLASTAPLGNDGLVMIPYFEGERTPNRPDATGAMHGFRLQNSTPAHFARAAIEGL 360

Query: 360 LCALADGLDALVAHGAEANRIVLVGGGARSEAVRRIAPALFGKPVLVPPPGEYVADGAAR 419
           LC LADG+D LV  G E  R++LVGGGA+S A+  IAPA+ G PV++P PGEYVA+GA R
Sbjct: 361 LCGLADGVDDLVRQGVEVKRVLLVGGGAKSLALCEIAPAILGVPVVIPAPGEYVAEGACR 420

Query: 420 QAAWVARGGDTPPAWSAASPEVYEDDPVPLIREQYAA 456
           QAAW   G   PP W       ++ +P P +RE+YA+
Sbjct: 421 QAAWALSGDTQPPVWPKPEERRFDAEPAPHVRERYAS 457


Lambda     K      H
   0.315    0.133    0.398 

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: 741
Number of extensions: 34
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: 466
Length of database: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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 WP_050654666.1 C1M55_RS22535 (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.3492555.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-119  386.1   0.0   1.3e-119  385.8   0.0    1.0  1  NCBI__GCF_002893965.1:WP_050654666.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002893965.1:WP_050654666.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  385.8   0.0  1.3e-119  1.3e-119       2     469 ..       6     455 ..       5     463 .. 0.93

  Alignments for each domain:
  == domain 1  score: 385.8 bits;  conditional E-value: 1.3e-119
                             TIGR01312   2 GiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisi 73 
                                           GiD +T+s+K+++ d ++ge++ +g+a+++v        E dp  wlea+++a++++         +++a+s+
  NCBI__GCF_002893965.1:WP_050654666.1   6 GIDSSTQSCKVIVRDaDSGELVREGRAAHPVG------TEIDPACWLEAMDSAIAAAGGL-----GDVAAVSV 67 
                                           9**************99***********9965......5***************998877.....57****** PP

                             TIGR01312  74 sGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnlalegfTapKllWvrkhepevf 145
                                           + Q+Hg+v LD  g+v+rpa+LWnDtr+a+++++l eelg  +++++++g +++++ Ta+Kl W+ +hep + 
  NCBI__GCF_002893965.1:WP_050654666.1  68 GAQQHGMVCLDSGGEVVRPALLWNDTRSAKAATDLVEELGgPKAWADAVGVVPVAAVTASKLRWLADHEPGNA 140
                                           ****************************************9******************************** PP

                             TIGR01312 146 ariakvlLPkDylrykLtgev.....vteysDAsGTllfdvkkrewskellka.ldleesllPklvessekaG 212
                                            r+a+v LP+D+l +kL g+      +t+ +DAsGT++++ ++re++k+ll+  +   +  +P++ +++ek+G
  NCBI__GCF_002893965.1:WP_050654666.1 141 DRTAAVCLPHDWLSWKLGGSGsieelATDAGDASGTGYYAASTREYRKDLLALaFRGRTPHVPRVASPNEKIG 213
                                           *****************99765555699**********************9962577799************* PP

                             TIGR01312 213 kvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalp 285
                                           ++r+      G     +v  G+gdnaa+A+Glg+v +g+v++s+GtSGvv av+ ++++dp g+v++F++a+ 
  NCBI__GCF_002893965.1:WP_050654666.1 214 STRS-----GG-----IVGPGTGDNAAAALGLGAV-PGDVIISIGTSGVVSAVSATPTHDPGGNVAGFADAT- 274
                                           *998.....45.....59***************66.9***********************************. PP

                             TIGR01312 286 gkwyplgvtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGlt.a 357
                                           g  +pl++tl+ +  l+ ++++lg +d +el ++a++++ g +g++++Py++GERtP++ p+a+g ++G + +
  NCBI__GCF_002893965.1:WP_050654666.1 275 GLHLPLVCTLNGARILDATASILG-VDHAELSRLASTAPLGNDGLVMIPYFEGERTPNR-PDATGAMHGFRlQ 345
                                           ************************.**********************************.***********99 PP

                             TIGR01312 358 nttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalG 430
                                           n+t a++arA++eg+  +l+d++d l + +g+++k++ l+GGGaks +  +i+  ilg++vv+p+  e++a G
  NCBI__GCF_002893965.1:WP_050654666.1 346 NSTPAHFARAAIEGLLCGLADGVDDLVR-QGVEVKRVLLVGGGAKSLALCEIAPAILGVPVVIPAPGEYVAEG 417
                                           99*********************99888.68****************************************** PP

                             TIGR01312 431 aAilAaialgekdlveecseavvkqkesvepiaenveay 469
                                           a ++Aa+al+ + +  + ++   ++ +  ep+ +  e+y
  NCBI__GCF_002893965.1:WP_050654666.1 418 ACRQAAWALSGDTQPPVWPKPEERRFDA-EPAPHVRERY 455
                                           *********9766655555554444333.5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (465 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: 17.91
//
[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:

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 2024 update 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