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

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.20754.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: 00:00:00.02
# Mc/sec: 11.09
//
[ok]

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

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Protein sequences (fasta format)
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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 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