GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Pseudomonas fluorescens FW300-N2E3

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate AO353_25905 AO353_25905 xylulose kinase

Query= reanno::pseudo6_N2E2:Pf6N2E2_805
         (495 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25905
          Length = 497

 Score =  805 bits (2080), Expect = 0.0
 Identities = 400/497 (80%), Positives = 437/497 (87%), Gaps = 2/497 (0%)

Query: 1   MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ 60
           M+ + LFLGIDCGTQGTKALILD+ SG+VLG GAAAHS+IS ANGRREQD  QWL+A T 
Sbjct: 1   MSIRNLFLGIDCGTQGTKALILDSRSGKVLGQGAAAHSLISSANGRREQDPAQWLEALTL 60

Query: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL 120
           AT QAL AA + G+ ILGIGVSGQQHGLVLLD+QGQVLRPAKLWCDTETT EN RLLAHL
Sbjct: 61  ATRQALLAANISGREILGIGVSGQQHGLVLLDEQGQVLRPAKLWCDTETTAENQRLLAHL 120

Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180
           GGE GSLERLGV IAPGYTVSKLLWT EQHPQ+F RIA +LLPHD+LNYWLTGR CSE+G
Sbjct: 121 GGESGSLERLGVAIAPGYTVSKLLWTEEQHPQIFARIAHILLPHDYLNYWLTGRCCSEFG 180

Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA 240
           DASGTGYFNVR+RQWD+QLL+ IDPS RLQAALPEL+EAHQ VG ILP IA  LGINP+A
Sbjct: 181 DASGTGYFNVRSRQWDLQLLRDIDPSGRLQAALPELLEAHQAVGTILPDIAERLGINPKA 240

Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL 300
           +VASGGGDNMMGA+GTGNIQPG ITMSLGSSGTVYAYA +P VSP  +VATFCSSSGGWL
Sbjct: 241 LVASGGGDNMMGALGTGNIQPGAITMSLGSSGTVYAYAEQPNVSPDAAVATFCSSSGGWL 300

Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS 360
           PLICTMNLTNAT A+REL DLD+  FNA V ++PIGAEGV MLPFLNGERVPALPHATGS
Sbjct: 301 PLICTMNLTNATSAVRELFDLDLSQFNARVEQSPIGAEGVSMLPFLNGERVPALPHATGS 360

Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA 420
           LLGL  +NLT+ANLCRAVVEGTTFGLRYGLDLLR NGLQ++SIRL GGGSKS  WRQ+VA
Sbjct: 361 LLGLNMSNLTQANLCRAVVEGTTFGLRYGLDLLRHNGLQSRSIRLTGGGSKSPAWRQMVA 420

Query: 421 DTMDTTVICTEQSEAAALGAAIQAAWCHS--GSQTGLAELCERCVKLDPSSETRPIAAHV 478
           D M+T V+CTE SEAAALGAAIQAAWC S  G+Q  L  LCERCV LDPSSET+P+AA+V
Sbjct: 421 DIMNTPVVCTEHSEAAALGAAIQAAWCESAAGTQQSLLALCERCVSLDPSSETQPVAANV 480

Query: 479 AASQQAYERYRQHVATL 495
           AA QQAYERYRQ VATL
Sbjct: 481 AAYQQAYERYRQQVATL 497


Lambda     K      H
   0.318    0.133    0.402 

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: 891
Number of extensions: 31
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: 495
Length of database: 497
Length adjustment: 34
Effective length of query: 461
Effective length of database: 463
Effective search space:   213443
Effective search space used:   213443
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 AO353_25905 AO353_25905 (xylulose kinase)
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.14399.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   8.6e-190  617.2   0.0   9.8e-190  617.0   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905  AO353_25905 xylulose kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905  AO353_25905 xylulose kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  617.0   0.0  9.8e-190  9.8e-190       1     479 [.       8     493 ..       8     495 .. 0.99

  Alignments for each domain:
  == domain 1  score: 617.0 bits;  conditional E-value: 9.8e-190
                                     TIGR01312   1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakee 64 
                                                   lGiD+gT+++Kal++d  +g+v+++g+a++++is+++g++Eqdp +wleal+ a++++l +a+ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905   8 LGIDCGTQGTKALILDsRSGKVLGQGAAAHSLISSANGRREQDPAQWLEALTLATRQALLAANIS 72 
                                                   7***************99*********************************************** PP

                                     TIGR01312  65 kkeikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnlaleg 128
                                                    +ei +i++sGQ+HglvlLDe+g+vlrpa+LW+Dt+t++e+++l ++lg e+ +le++g ++++g
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905  73 GREILGIGVSGQQHGLVLLDEQGQVLRPAKLWCDTETTAENQRLLAHLGgESGSLERLGVAIAPG 137
                                                   *************************************************9*************** PP

                                     TIGR01312 129 fTapKllWvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellka 193
                                                   +T++KllW+ +++p++faria++lLP+Dyl+y+Ltg+ ++e +DAsGT++f+v+ r+w+ +ll+ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 138 YTVSKLLWTEEQHPQIFARIAHILLPHDYLNYWLTGRCCSEFGDASGTGYFNVRSRQWDLQLLRD 202
                                                   ***************************************************************** PP

                                     TIGR01312 194 ldle...esllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvs 255
                                                   +d++   +++lP+l+e+++ +G++ +++a++lG++ +  va+Gggdn++gA+G+g++++g++++s
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 203 IDPSgrlQAALPELLEAHQAVGTILPDIAERLGINPKALVASGGGDNMMGALGTGNIQPGAITMS 267
                                                   ****99999******************************************************** PP

                                     TIGR01312 256 lGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneea 320
                                                   lG+SG+v+a++++++++p++av++Fc+++ g+w+pl++t+++t+a++ ++el+  ld++++n+ +
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 268 LGSSGTVYAYAEQPNVSPDAAVATFCSSS-GGWLPLICTMNLTNATSAVRELFD-LDLSQFNARV 330
                                                   *****************************.************************.********** PP

                                     TIGR01312 321 ekvevgaegvlllPylsGERtPhldpqargsliGlt.anttradlarAvlegvafalrdsldilk 384
                                                   e++++gaegv++lP+l+GER+P+l p+a+gsl+Gl+ +n t+a+l+rAv+eg++f+lr++ld+l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 331 EQSPIGAEGVSMLPFLNGERVPAL-PHATGSLLGLNmSNLTQANLCRAVVEGTTFGLRYGLDLLR 394
                                                   ************************.***********8999************************* PP

                                     TIGR01312 385 elkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalGaAilAaialg....ekdlv 445
                                                   + +gl++++irl+GGG+ks++wrq++adi++++vv++e++e+aalGaAi+Aa++++    +++l+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 395 H-NGLQSRSIRLTGGGSKSPAWRQMVADIMNTPVVCTEHSEAAALGAAIQAAWCESaagtQQSLL 458
                                                   *.88**************************************************99888778899 PP

                                     TIGR01312 446 eecseavvkqkes.vepiaenveayeelyerykkl 479
                                                   ++c+++v+ + +s ++p+a+nv+ay+++yery++ 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_25905 459 ALCERCVSLDPSSeTQPVAANVAAYQQAYERYRQQ 493
                                                   **********9999******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (497 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: 00:00:00.01
# Mc/sec: 11.98
//
[ok]

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

Links

Downloads

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:

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