Alignments for a candidate for xylB in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylB in Herbaspirillum seropedicae SmR1

Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate HSERO_RS02220 HSERO_RS02220 xylulokinase

Query= CharProtDB::CH_003784
         (484 letters)



>FitnessBrowser__HerbieS:HSERO_RS02220
          Length = 490

 Score =  496 bits (1277), Expect = e-145
 Identities = 257/488 (52%), Positives = 327/488 (67%), Gaps = 9/488 (1%)

Query: 1   MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKALG 60
           MY+GIDLGTS VK ++++ QG +VA     L V+RPHP WSEQ P  WWQAT   +  L 
Sbjct: 1   MYLGIDLGTSEVKAVVIDAQGSLVALAGSTLNVARPHPRWSEQAPADWWQATCDTVAKLR 60

Query: 61  DQHSLQ---DVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQSRV 117
            Q   +    ++A+G++GQMHGA LLD +  VLRPAILW+D R A EC  LE+R P+   
Sbjct: 61  TQLGSERFGSIRAIGLSGQMHGAVLLDERDEVLRPAILWSDSRSAPECAELESRAPRLHG 120

Query: 118 ITGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTMWL 177
           I GNL MPGFTAPKLLWV RHEP++F +I  VLLPKD+LRL+MTG   SD SDAAGT+WL
Sbjct: 121 IAGNLAMPGFTAPKLLWVARHEPQLFARIATVLLPKDWLRLKMTGRKVSDPSDAAGTLWL 180

Query: 178 DVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGG-GDNAA 236
           DV  R+WSD +L A  + RDQMPAL +GS ++G+LLPEVA+AWG+ +  +VAGG GD AA
Sbjct: 181 DVEGRNWSDELLAASGMRRDQMPALVDGSAVSGSLLPEVAQAWGLRSDVIVAGGAGDGAA 240

Query: 237 GAVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAAS 296
            AVG+G V      LSLGTSGV F V++ F   P  A+H+FCH LPQRWH MSVMLSAAS
Sbjct: 241 SAVGIGAVKPGDGFLSLGTSGVLFVVNDRFRPNPGRAIHAFCHTLPQRWHQMSVMLSAAS 300

Query: 297 CLDWAAKLTGLSNVPALIAAAQQADESA--EPVWFLPYLSGERTPHNNPQAKGVFFGLTH 354
           CL W  +L  +    +L+A  +Q DE A      FLPYLSGERTPHN+P A GVF GLT 
Sbjct: 301 CLRWFCRLCSVDE-KSLLAEIEQLDEQACNNAPLFLPYLSGERTPHNDPYATGVFHGLTP 359

Query: 355 QHGPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQL 414
           +H    L  AVLEGV + + DG+D + A G     ++L+GGGARS YW Q+LAD    ++
Sbjct: 360 EHQRAALGYAVLEGVAFGMVDGLDALRAAGTDVAELSLVGGGARSAYWAQLLADALQVRI 419

Query: 415 DYRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAYQPRRETFRR 474
               G + G ALGAARLA +A   +++  E+  +   +  + PD  R+AA Q R + +R 
Sbjct: 420 VTHVGSEAGGALGAARLAWLADGGDEA--EVCRKPAQQALYQPDPARHAALQARLQRYRA 477

Query: 475 LYQQLLPL 482
           +Y    PL
Sbjct: 478 IYAPFAPL 485


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: 718
Number of extensions: 24
Number of successful extensions: 5
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: 490
Length adjustment: 34
Effective length of query: 450
Effective length of database: 456
Effective search space:   205200
Effective search space used:   205200
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 HSERO_RS02220 HSERO_RS02220 (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.12379.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   8.4e-178  577.7   0.0   9.5e-178  577.5   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS02220  HSERO_RS02220 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS02220  HSERO_RS02220 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.5   0.0  9.5e-178  9.5e-178       1     480 [.       3     479 ..       3     480 .. 0.97

  Alignments for each domain:
  == domain 1  score: 577.5 bits;  conditional E-value: 9.5e-178
                                  TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekak.eekke 67 
                                                lGiDlgTs+vKa+++d++g+++a + + l+v++p+p wsEq p +w++a+++++++l+++   e+  +
  lcl|FitnessBrowser__HerbieS:HSERO_RS02220   3 LGIDLGTSEVKAVVIDAQGSLVALAGSTLNVARPHPRWSEQAPADWWQATCDTVAKLRTQLGsERFGS 70 
                                                7********************************************************9997615689* PP

                                  TIGR01312  68 ikaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKll 135
                                                i+ai++sGQmHg+vlLDe ++vlrpaiLW D r+a ec+ele++++  +l+ ++gnla++gfTapKll
  lcl|FitnessBrowser__HerbieS:HSERO_RS02220  71 IRAIGLSGQMHGAVLLDERDEVLRPAILWSDSRSAPECAELESRAP--RLHGIAGNLAMPGFTAPKLL 136
                                                *********************************************9..******************** PP

                                  TIGR01312 136 WvrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPk 203
                                                Wv +hep+ faria+vlLPkD+lr+k+tg++v++ sDA+GTl++dv+ r+ws+ell+a  + ++++P+
  lcl|FitnessBrowser__HerbieS:HSERO_RS02220 137 WVARHEPQLFARIATVLLPKDWLRLKMTGRKVSDPSDAAGTLWLDVEGRNWSDELLAASGMRRDQMPA 204
                                                ******************************************************************** PP

                                  TIGR01312 204 lvessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaes 271
                                                lv++s+++G++ +eva+++Gl ++v+va+G+gd aa+A+G+g+vk+g+ ++slGtSGv+++v+d+ ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS02220 205 LVDGSAVSGSLLPEVAQAWGLRSDVIVAGGAGDGAASAVGIGAVKPGDGFLSLGTSGVLFVVNDRFRP 272
                                                ******************************************************************** PP

                                  TIGR01312 272 dpegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekvevga..egvlllPyls 337
                                                +p  a+h+Fch+lp++w++++v+lsa+s+l w+++l + +d ++l++e+e+ +++a  ++ l+lPyls
  lcl|FitnessBrowser__HerbieS:HSERO_RS02220 273 NPGRAIHAFCHTLPQRWHQMSVMLSAASCLRWFCRLCS-VDEKSLLAEIEQLDEQAcnNAPLFLPYLS 339
                                                *************************************9.************988744499******** PP

                                  TIGR01312 338 GERtPhldpqargsliGltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksev 405
                                                GERtPh+dp a+g+++Glt +++ra l +Avlegvaf++ d+ld+l++ +g++++e++l+GGGa+s++
  lcl|FitnessBrowser__HerbieS:HSERO_RS02220 340 GERTPHNDPYATGVFHGLTPEHQRAALGYAVLEGVAFGMVDGLDALRA-AGTDVAELSLVGGGARSAY 406
                                                ************************************************.67***************** PP

                                  TIGR01312 406 wrqiladilglevvvpe.eeegaalGaAilAaialgekdlveecseavvkqkesvepiaenveayeel 472
                                                w q+lad l++++v++  +e g alGaA+lA +a g  d++e+c++    q++ ++p+ ++++a + +
  lcl|FitnessBrowser__HerbieS:HSERO_RS02220 407 WAQLLADALQVRIVTHVgSEAGGALGAARLAWLADGG-DEAEVCRKPA--QQALYQPDPARHAALQAR 471
                                                ***************9978999*********999986.7999999975..455578************ PP

                                  TIGR01312 473 yerykkly 480
                                                ++ry+++y
  lcl|FitnessBrowser__HerbieS:HSERO_RS02220 472 LQRYRAIY 479
                                                *****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (490 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: 12.39
//
[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