Alignments for a candidate for xylB in Neiella marina J221

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Neiella marina J221

Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate WP_087504365.1 CBE68_RS00090 xylulokinase

Query= CharProtDB::CH_003784
         (484 letters)



>NCBI__GCF_002165625.1:WP_087504365.1
          Length = 483

 Score =  639 bits (1649), Expect = 0.0
 Identities = 302/478 (63%), Positives = 377/478 (78%)

Query: 1   MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG 60
           MYIGIDLGTSGVKV++L++Q +VVA++T  L +SRP+PLWSEQDP+ WW AT +A+ +L 
Sbjct: 1   MYIGIDLGTSGVKVVVLSDQDQVVASETVALPISRPYPLWSEQDPKDWWDATVQAVDSLK 60

Query: 61  DQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRVITG 120
               L  V A+G++GQMHGATLLD    VLRPAILWNDGRCA+EC L+E +VP +R ITG
Sbjct: 61  AGGHLSQVTAIGMSGQMHGATLLDKDGEVLRPAILWNDGRCAEECELIEQQVPAARDITG 120

Query: 121 NLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWLDVA 180
           N++MPGFTAPKLLWV+RHE ++F +I KVLLPKDYLR ++TG+FASDMSD+AGT W+DV 
Sbjct: 121 NIVMPGFTAPKLLWVKRHEADVFEKISKVLLPKDYLRFKLTGDFASDMSDSAGTSWMDVG 180

Query: 181 KRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNAAGAVG 240
           KRDWS+ ML AC L+R+QMP L+EGSE+TG L  E+A+ WG+  + V+AGGGDNAAGAVG
Sbjct: 181 KRDWSEPMLSACGLTREQMPQLFEGSEVTGYLSEELAERWGLGKIAVIAGGGDNAAGAVG 240

Query: 241 VGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAASCLDW 300
           VG+    QAMLSLGTSGVYFAVS+GF + P+SAVH+FCHALP  WHLMSV LSAA+C  W
Sbjct: 241 VGLTKPGQAMLSLGTSGVYFAVSDGFNANPDSAVHAFCHALPDTWHLMSVHLSAAACNAW 300

Query: 301 AAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQHGPNE 360
              +TG + VP +     +     +  +FLPYLSGERTPHNNP AKG+FFGLTH+     
Sbjct: 301 LDSVTGKTGVPEMFEEVSRFTPQKDDPYFLPYLSGERTPHNNPNAKGMFFGLTHETDRAA 360

Query: 361 LARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLDYRTGG 420
           +ARAVLEGVG+A ADG D +HA G+KP  V+LIGGGAR++ WRQMLA+I  Q L YR GG
Sbjct: 361 MARAVLEGVGFAFADGFDALHASGVKPDEVSLIGGGARNQNWRQMLANILNQTLVYRQGG 420

Query: 421 DVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRRLYQQ 478
           DVGPALGAARLA++A NPE  + E+ P   L ++H P+A++ A YQ RRETFR+LY++
Sbjct: 421 DVGPALGAARLARLAMNPELDMAEICPVPELVETHTPEAEQVAVYQERRETFRKLYER 478


Lambda     K      H
   0.319    0.134    0.409 

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: 717
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: 484
Length of database: 483
Length adjustment: 34
Effective length of query: 450
Effective length of database: 449
Effective search space:   202050
Effective search space used:   202050
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 WP_087504365.1 CBE68_RS00090 (xylulokinase)
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.101425.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.7e-185  601.6   0.0   5.3e-185  601.4   0.0    1.0  1  NCBI__GCF_002165625.1:WP_087504365.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002165625.1:WP_087504365.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  601.4   0.0  5.3e-185  5.3e-185       1     481 []       3     477 ..       3     477 .. 0.99

  Alignments for each domain:
  == domain 1  score: 601.4 bits;  conditional E-value: 5.3e-185
                             TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkeikaisi 73 
                                           +GiDlgTs+vK+++++++ +v+as++ +l++++p p wsEqdp++w++a+ +a+++l++  +   ++++ai++
  NCBI__GCF_002165625.1:WP_087504365.1   3 IGIDLGTSGVKVVVLSDQDQVVASETVALPISRPYPLWSEQDPKDWWDATVQAVDSLKAGGH--LSQVTAIGM 73 
                                           8********************************************************99866..69******* PP

                             TIGR01312  74 sGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllWvrkhepevfa 146
                                           sGQmHg++lLD++g+vlrpaiLWnD r+aeece +e++++  +++++tgn++++gfTapKllWv++he +vf+
  NCBI__GCF_002165625.1:WP_087504365.1  74 SGQMHGATLLDKDGEVLRPAILWNDGRCAEECELIEQQVP--AARDITGNIVMPGFTAPKLLWVKRHEADVFE 144
                                           ***************************************9..9****************************** PP

                             TIGR01312 147 riakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPklvessekaGkvreeva 219
                                           +i+kvlLPkDylr+kLtg++++++sD++GT + dv kr+ws+ +l+a+ l ++++P+l+e+se++G ++ee+a
  NCBI__GCF_002165625.1:WP_087504365.1 145 KISKVLLPKDYLRFKLTGDFASDMSDSAGTSWMDVGKRDWSEPMLSACGLTREQMPQLFEGSEVTGYLSEELA 217
                                           ************************************************************************* PP

                             TIGR01312 220 kklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesdpegavhsFchalpgkwyplg 292
                                           +++Gl  ++ v+aGggdnaagA+G+g +k+g++++slGtSGv++av+d  +++p++avh+Fchalp++w+ ++
  NCBI__GCF_002165625.1:WP_087504365.1 218 ERWGL-GKIAVIAGGGDNAAGAVGVGLTKPGQAMLSLGTSGVYFAVSDGFNANPDSAVHAFCHALPDTWHLMS 289
                                           *****.89***************************************************************** PP

                             TIGR01312 293 vtlsatsalewlkellgeldveelneeaekvevgaegvlllPylsGERtPhldpqargsliGltanttradla 365
                                           v lsa++++ wl +++g++ v e+ ee+++ +++ +   +lPylsGERtPh++p+a+g+++Glt++t ra +a
  NCBI__GCF_002165625.1:WP_087504365.1 290 VHLSAAACNAWLDSVTGKTGVPEMFEEVSRFTPQKDDPYFLPYLSGERTPHNNPNAKGMFFGLTHETDRAAMA 362
                                           ************************************************************************* PP

                             TIGR01312 366 rAvlegvafalrdsldilkelkglkikeirliGGGaksevwrqiladilglevvvpe.eeegaalGaAilAai 437
                                           rAvlegv fa++d++d+l++ +g+k++e++liGGGa+++ wrq+la+il++++v+++  + g+alGaA+lA +
  NCBI__GCF_002165625.1:WP_087504365.1 363 RAVLEGVGFAFADGFDALHA-SGVKPDEVSLIGGGARNQNWRQMLANILNQTLVYRQgGDVGPALGAARLARL 434
                                           ********************.88*********************************999************** PP

                             TIGR01312 438 alg.ekdlveecseavvkqkesvepiaenveayeelyerykklye 481
                                           a++ e d++e c+     ++++  p+ae+v+ y+e+ e+++klye
  NCBI__GCF_002165625.1:WP_087504365.1 435 AMNpELDMAEICPVPELVETHT--PEAEQVAVYQERRETFRKLYE 477
                                           ***9999999**9999999999..*******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (483 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 28.42
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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