GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Tatumella morbirosei LMG 23360

Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate WP_038015560.1 HA49_RS17420 xylulokinase

Query= CharProtDB::CH_003784
         (484 letters)



>NCBI__GCF_000757425.2:WP_038015560.1
          Length = 489

 Score =  504 bits (1299), Expect = e-147
 Identities = 258/484 (53%), Positives = 326/484 (67%), Gaps = 6/484 (1%)

Query: 1   MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG 60
           MY+GID+GTS +K ++++EQG++VA    +LT+ RPHP WSEQDP+ WWQA  RAM  L 
Sbjct: 1   MYLGIDVGTSEIKTLVIDEQGKIVAFAGAELTIQRPHPHWSEQDPQSWWQALQRAMGQLR 60

Query: 61  DQHS--LQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVI 118
           ++ +     +KA+G++GQMHGA LLD Q  VLRP ILWND R A++C  L A+ P    I
Sbjct: 61  EKAAEHWSSIKAIGLSGQMHGAVLLDKQGEVLRPCILWNDTRSAEQCQQLTAKAPSLHRI 120

Query: 119 TGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLD 178
            GNL MPGFTAPKLLWV RHEP+IF +I  VLLPKDYLR RMTGEF SDMSD+AGT+WLD
Sbjct: 121 AGNLAMPGFTAPKLLWVARHEPDIFARIAHVLLPKDYLRWRMTGEFISDMSDSAGTLWLD 180

Query: 179 VAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGM-ATVPVVAGGGDNAAG 237
           VAKRDWSD +LQACDL+R+ MPAL EGS   G L PE+A  W + A + V  GGGDNAA 
Sbjct: 181 VAKRDWSDELLQACDLTREMMPALVEGSAAGGRLTPEIAAEWHLPAGLVVAGGGGDNAAS 240

Query: 238 AVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASC 297
           AVG+G V    A +SLGTSGV F V+E +   P+SAVH+FCHALPQRWH MSVMLSAAS 
Sbjct: 241 AVGIGAVRPGDAFISLGTSGVLFTVNECYRPNPQSAVHAFCHALPQRWHQMSVMLSAASA 300

Query: 298 LDWAAKLTGLSNVPALIAAAQ-QADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQH 356
           L W  ++ G      +    +   D+      FLPYLSGERTPHN+PQA G F  LTH  
Sbjct: 301 LRWVCQILGCDETTLMAEVGRLTLDQRRNAPIFLPYLSGERTPHNDPQASGSFHYLTHDV 360

Query: 357 GPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDY 416
               L  AV+EG+ + LADG+ V++  G +    +L+GGGARS  W Q++AD+    +  
Sbjct: 361 TRAHLGYAVIEGITFGLADGLRVLNEAGTELSECSLVGGGARSAEWSQLIADVLNLPMIT 420

Query: 417 RTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLY 476
             G + G ALGAARLA +A   +++ + + P    +Q   P A  +   Q R + FR +Y
Sbjct: 421 HEGSEAGGALGAARLAWLADGGDEAQVCVKP--AEKQRFQPQADHWEYLQKRLKAFRLMY 478

Query: 477 QQLL 480
           QQ L
Sbjct: 479 QQQL 482


Lambda     K      H
   0.319    0.134    0.409 

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: 712
Number of extensions: 35
Number of successful extensions: 5
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: 489
Length adjustment: 34
Effective length of query: 450
Effective length of database: 455
Effective search space:   204750
Effective search space used:   204750
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: 52 (24.6 bits)

Align candidate WP_038015560.1 HA49_RS17420 (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.2971122.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.8e-187  609.6   0.0     2e-187  609.4   0.0    1.0  1  NCBI__GCF_000757425.2:WP_038015560.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000757425.2:WP_038015560.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  609.4   0.0    2e-187    2e-187       1     480 [.       3     478 ..       3     479 .. 0.97

  Alignments for each domain:
  == domain 1  score: 609.4 bits;  conditional E-value: 2e-187
                             TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisi 73 
                                           lGiD+gTs++K+l++de+g+++a + a+lt+++p+p+wsEqdp++w++al++a+ +l+eka+e++++ikai++
  NCBI__GCF_000757425.2:WP_038015560.1   3 LGIDVGTSEIKTLVIDEQGKIVAFAGAELTIQRPHPHWSEQDPQSWWQALQRAMGQLREKAAEHWSSIKAIGL 75 
                                           7************************************************************************ PP

                             TIGR01312  74 sGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfa 146
                                           sGQmHg+vlLD++g+vlrp+iLWnDtr+ae+c++l+++++  +l++++gnla++gfTapKllWv +hep++fa
  NCBI__GCF_000757425.2:WP_038015560.1  76 SGQMHGAVLLDKQGEVLRPCILWNDTRSAEQCQQLTAKAP--SLHRIAGNLAMPGFTAPKLLWVARHEPDIFA 146
                                           ***************************************9..******************************* PP

                             TIGR01312 147 riakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreeva 219
                                           ria+vlLPkDylr+++tge+++++sD++GTl++dv+kr+ws+ell+a+dl ++++P+lve+s+  G++++e+a
  NCBI__GCF_000757425.2:WP_038015560.1 147 RIAHVLLPKDYLRWRMTGEFISDMSDSAGTLWLDVAKRDWSDELLQACDLTREMMPALVEGSAAGGRLTPEIA 219
                                           ************************************************************************* PP

                             TIGR01312 220 kklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplg 292
                                           +++ l +g  va+Gggdnaa+A+G+g+v++g++++slGtSGv+++v++ ++++p++avh+Fchalp++w++++
  NCBI__GCF_000757425.2:WP_038015560.1 220 AEWHLPAGLVVAGGGGDNAASAVGIGAVRPGDAFISLGTSGVLFTVNECYRPNPQSAVHAFCHALPQRWHQMS 292
                                           ************************************************************************* PP

                             TIGR01312 293 vtlsatsalewlkellgeldveelneeaekvevg..aegvlllPylsGERtPhldpqargsliGltanttrad 363
                                           v+lsa+sal w++++lg  d ++l++e+ + + +   ++ ++lPylsGERtPh+dpqa+gs++ lt++ tra+
  NCBI__GCF_000757425.2:WP_038015560.1 293 VMLSAASALRWVCQILG-CDETTLMAEVGRLTLDqrRNAPIFLPYLSGERTPHNDPQASGSFHYLTHDVTRAH 364
                                           *****************.89999999999887664489*********************************** PP

                             TIGR01312 364 larAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilA 435
                                           l +Av+eg++f+l+d+l +l+e +g++++e++l+GGGa+s+ w q++ad+l+l++ ++e +e g alGaA+lA
  NCBI__GCF_000757425.2:WP_038015560.1 365 LGYAVIEGITFGLADGLRVLNE-AGTELSECSLVGGGARSAEWSQLIADVLNLPMITHEgSEAGGALGAARLA 436
                                           **********************.67*********************************988999********* PP

                             TIGR01312 436 aialgekdlveecseavvkqkesvepiaenveayeelyerykkly 480
                                            +a g  d++++c +   kq+   +p+a + e  +++++ ++ +y
  NCBI__GCF_000757425.2:WP_038015560.1 437 WLADGG-DEAQVCVKPAEKQR--FQPQADHWEYLQKRLKAFRLMY 478
                                           999986.78999988876665..5599999999999999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (489 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 0.02s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 13.12
//
[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