GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Pseudomonas fluorescens FW300-N2E2

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate Pf6N2E2_805 Xylulose kinase (EC 2.7.1.17)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805
          Length = 495

 Score =  991 bits (2563), Expect = 0.0
 Identities = 495/495 (100%), Positives = 495/495 (100%)

Query: 1   MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ 60
           MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ
Sbjct: 1   MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ 60

Query: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL 120
           ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL
Sbjct: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL 120

Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180
           GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG
Sbjct: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180

Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA 240
           DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA
Sbjct: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA 240

Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL 300
           VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL
Sbjct: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL 300

Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS 360
           PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS
Sbjct: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS 360

Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA 420
           LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA
Sbjct: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA 420

Query: 421 DTMDTTVICTEQSEAAALGAAIQAAWCHSGSQTGLAELCERCVKLDPSSETRPIAAHVAA 480
           DTMDTTVICTEQSEAAALGAAIQAAWCHSGSQTGLAELCERCVKLDPSSETRPIAAHVAA
Sbjct: 421 DTMDTTVICTEQSEAAALGAAIQAAWCHSGSQTGLAELCERCVKLDPSSETRPIAAHVAA 480

Query: 481 SQQAYERYRQHVATL 495
           SQQAYERYRQHVATL
Sbjct: 481 SQQAYERYRQHVATL 495


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: 1070
Number of extensions: 32
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate Pf6N2E2_805 (Xylulose kinase (EC 2.7.1.17))
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.24773.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   3.3e-188  612.0   0.1   3.7e-188  611.8   0.1    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805  Xylulose kinase (EC 2.7.1.17)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805  Xylulose kinase (EC 2.7.1.17)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  611.8   0.1  3.7e-188  3.7e-188       1     480 [.       8     492 ..       8     493 .. 0.99

  Alignments for each domain:
  == domain 1  score: 611.8 bits;  conditional E-value: 3.7e-188
                                     TIGR01312   1 lGiDlgTssvKallvd.ekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakee 64 
                                                   lGiD+gT+++Kal++d  +g+v++ g+a++++is ++g++Eqd+++wl+a+++a++++l++a ++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805   8 LGIDCGTQGTKALILDaTSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQATHQALAAAGVD 72 
                                                   7***************999********************************************** PP

                                     TIGR01312  65 kkeikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelg.eeelleltgnlaleg 128
                                                    ++i +i++sGQ+HglvlLD++g+vlrpa+LW+Dt+t+ e+++l ++lg e+ +le++g ++++g
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805  73 GQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHLGgEDGSLERLGVVIAPG 137
                                                   *************************************************9*************** PP

                                     TIGR01312 129 fTapKllWvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellka 193
                                                   +T++KllW+r+++p+vf+ria+vlLP+D+l+y+Ltg++++ey+DAsGT++f+v++r+w+ +ll++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805 138 YTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYGDASGTGYFNVRTRQWDVQLLQH 202
                                                   ***************************************************************** PP

                                     TIGR01312 194 ldle...esllPklvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvs 255
                                                   +d++   +++lP+l+e+++ +G++ +++a++lG++ +  va+Gggdn++gAiG+g++++g++++s
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805 203 IDPSarlQAALPELIEAHQPVGRILPAIAAHLGINPEAVVASGGGDNMMGAIGTGNIQPGVITMS 267
                                                   ****999999******************************************************* PP

                                     TIGR01312 256 lGtSGvvlavedkaesdpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneea 320
                                                   lG+SG+v+a++ ++ ++p+ +v++Fc+++ g+w+pl++t+++t+a+  ++ell  ld++++n+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805 268 LGSSGTVYAYAAEPAVSPQPSVATFCSSS-GGWLPLICTMNLTNATGAIRELLD-LDIDAFNALV 330
                                                   *****************************.***********************9.********** PP

                                     TIGR01312 321 ekvevgaegvlllPylsGERtPhldpqargsliGlt.anttradlarAvlegvafalrdsldilk 384
                                                   +k+++gaegv++lP+l+GER+P+l p+a+gsl+Glt +n tra+l+rAv+eg++f+lr++ld+l+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805 331 AKAPIGAEGVCMLPFLNGERVPAL-PHATGSLLGLTtTNLTRANLCRAVVEGTTFGLRYGLDLLR 394
                                                   ************************.***********899************************** PP

                                     TIGR01312 385 elkglkikeirliGGGaksevwrqiladilglevvvpeeeegaalGaAilAaialg..ekdlvee 447
                                                   + +gl+ ++irliGGG+ks++wrqi+ad ++++v ++e++e+aalGaAi+Aa++ +  ++ l+e+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805 395 A-NGLQAQSIRLIGGGSKSAQWRQIVADTMDTTVICTEQSEAAALGAAIQAAWCHSgsQTGLAEL 458
                                                   *.88***************************************************97777799** PP

                                     TIGR01312 448 cseavvkqkes.vepiaenveayeelyerykkly 480
                                                   c+++v+ + +s ++pia++v+a +++yery++++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805 459 CERCVKLDPSSeTRPIAAHVAASQQAYERYRQHV 492
                                                   ********9999*******************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 11.91
//
[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