GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Pseudomonas fluorescens FW300-N2C3

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate AO356_27695 AO356_27695 xylulose kinase

Query= reanno::pseudo5_N2C3_1:AO356_27695
         (495 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27695
          Length = 495

 Score =  993 bits (2566), Expect = 0.0
 Identities = 495/495 (100%), Positives = 495/495 (100%)

Query: 1   MANQQLFLGIDCGTQGTKALILDTISGQVLGQGAAAHSMISGANGRREQDTQQWLDAFTQ 60
           MANQQLFLGIDCGTQGTKALILDTISGQVLGQGAAAHSMISGANGRREQDTQQWLDAFTQ
Sbjct: 1   MANQQLFLGIDCGTQGTKALILDTISGQVLGQGAAAHSMISGANGRREQDTQQWLDAFTQ 60

Query: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAYL 120
           ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAYL
Sbjct: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAYL 120

Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180
           GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG
Sbjct: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180

Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPDA 240
           DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPDA
Sbjct: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPDA 240

Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSNGGWL 300
           VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSNGGWL
Sbjct: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSNGGWL 300

Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVVQAPIGAEGVCMLPFLNGERVPALPHATAS 360
           PLICTMNLTNATGAIRELLDLDIDAFNALVVQAPIGAEGVCMLPFLNGERVPALPHATAS
Sbjct: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVVQAPIGAEGVCMLPFLNGERVPALPHATAS 360

Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLKAQSIRLIGGGSKSPVWRQIVA 420
           LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLKAQSIRLIGGGSKSPVWRQIVA
Sbjct: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLKAQSIRLIGGGSKSPVWRQIVA 420

Query: 421 DIMDTTVICTEQSEAAALGAAIQAAWCHSGAQDSLAELCERCVKLDPASETRPVTAHVTA 480
           DIMDTTVICTEQSEAAALGAAIQAAWCHSGAQDSLAELCERCVKLDPASETRPVTAHVTA
Sbjct: 421 DIMDTTVICTEQSEAAALGAAIQAAWCHSGAQDSLAELCERCVKLDPASETRPVTAHVTA 480

Query: 481 SQQAYERYRQHVATL 495
           SQQAYERYRQHVATL
Sbjct: 481 SQQAYERYRQHVATL 495


Lambda     K      H
   0.319    0.134    0.405 

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: 1036
Number of extensions: 25
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: 495
Length of database: 495
Length adjustment: 34
Effective length of query: 461
Effective length of database: 461
Effective search space:   212521
Effective search space used:   212521
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 AO356_27695 AO356_27695 (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.3908103.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-188  612.9   0.1   2.1e-188  612.7   0.1    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695  AO356_27695 xylulose kinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695  AO356_27695 xylulose kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  612.7   0.1  2.1e-188  2.1e-188       1     480 [.       8     492 ..       8     493 .. 0.99

  Alignments for each domain:
  == domain 1  score: 612.7 bits;  conditional E-value: 2.1e-188
                                       TIGR01312   1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekak 62 
                                                     lGiD+gT+++Kal++d  +g+v+++g+a++++is ++g++Eqd+++wl+a+++a++++l++a 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695   8 LGIDCGTQGTKALILDtISGQVLGQGAAAHSMISGANGRREQDTQQWLDAFTQATHQALAAAG 70 
                                                     7***************99********************************************* PP

                                       TIGR01312  63 eekkeikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnl 124
                                                     ++ ++i +i++sGQ+HglvlLD++g+vlrpa+LW+Dt+t+ e+++l ++lg e+ +le++g +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695  71 VDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAYLGgEDGSLERLGVV 133
                                                     *************************************************************** PP

                                       TIGR01312 125 alegfTapKllWvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrews 187
                                                     +++g+T++KllW+r+++p+vf+ria+vlLP+D+l+y+Ltg++++ey+DAsGT++f+v++r+w+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695 134 IAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYGDASGTGYFNVRTRQWD 196
                                                     *************************************************************** PP

                                       TIGR01312 188 kellkaldle...esllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgiv 247
                                                      +ll+++d++   +++lP+l+e+++ +G++ +++a++lG++ +  va+Gggdn++gAiG+g++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695 197 VQLLQHIDPSarlQAALPELIEAHQPVGRILPAIAAHLGINPDAVVASGGGDNMMGAIGTGNI 259
                                                     **********999999*********************************************** PP

                                       TIGR01312 248 kegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellge 310
                                                     ++g++++slG+SG+v+a++ ++ ++p+ +v++Fc+++ g+w+pl++t+++t+a+  ++ell  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695 260 QPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSN-GGWLPLICTMNLTNATGAIRELLD- 320
                                                     *************************************.***********************9. PP

                                       TIGR01312 311 ldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGlt.anttradlarAvlegv 372
                                                     ld++++n+++ ++++gaegv++lP+l+GER+P+l p+a++sl+Glt +n tra+l+rAv+eg+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695 321 LDIDAFNALVVQAPIGAEGVCMLPFLNGERVPAL-PHATASLLGLTtTNLTRANLCRAVVEGT 382
                                                     **********************************.***********899************** PP

                                       TIGR01312 373 afalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalGaAilA 435
                                                     +f+lr++ld+l++ +glk ++irliGGG+ks+vwrqi+adi++++v ++e++e+aalGaAi+A
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695 383 TFGLRYGLDLLRA-NGLKAQSIRLIGGGSKSPVWRQIVADIMDTTVICTEQSEAAALGAAIQA 444
                                                     *************.88*********************************************** PP

                                       TIGR01312 436 aialg..ekdlveecseavvkqkes.vepiaenveayeelyerykkly 480
                                                     a++ +  +++l+e+c+++v+ + +s ++p++++v+a +++yery++++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27695 445 AWCHSgaQDSLAELCERCVKLDPASeTRPVTAHVTASQQAYERYRQHV 492
                                                     ****987778999********99999*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (495 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 26.58
//
[ok]

This GapMind analysis is from Sep 17 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