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

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.1039.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 8.85
//
[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:

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