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 Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate HSERO_RS17030 HSERO_RS17030 xylulokinase

Query= reanno::Smeli:SMc03164
         (484 letters)



>FitnessBrowser__HerbieS:HSERO_RS17030
          Length = 493

 Score =  485 bits (1248), Expect = e-141
 Identities = 259/486 (53%), Positives = 313/486 (64%), Gaps = 9/486 (1%)

Query: 2   YLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLRE 61
           YLG+DLGTS VK +L D +  +I S S  L VD PHP WSEQ P  W  A  +AIA LR 
Sbjct: 3   YLGIDLGTSEVKLVLTDEDSNVIASTSARLRVDNPHPLWSEQAPQSWWNATLDAIAALRT 62

Query: 62  THAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALDG-DPQFRALT 120
              QA  A+RGIGLSGQMHGATLLD    VLRP ILWND R+  E   L+   P   A+T
Sbjct: 63  QAPQAFQALRGIGLSGQMHGATLLDRNGNVLRPAILWNDMRAHAECVELEALVPDAVAIT 122

Query: 121 GNIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLDT 180
           GN   PGFTAPKL W+ + EP ++  +  VLLPKD+L   LTGE +SEMSD+AGT WLD 
Sbjct: 123 GNRAMPGFTAPKLLWLSKYEPAVYRAIDKVLLPKDFLGWKLTGEFVSEMSDAAGTLWLDV 182

Query: 181 GKRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAASA 240
            +R WS  +L AT L+   MP LVEG+  AG LR EL   WG+   VVVAGGAGDNAASA
Sbjct: 183 ARRDWSERMLGATGLDRSHMPRLVEGSAVAGQLRDELRREWGISGPVVVAGGAGDNAASA 242

Query: 241 CGMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDAL 300
            G+G +  G AF+SLG+SGVLFAA A + PN +  VHAFCH LP  WHQM VILSA  +L
Sbjct: 243 VGIGVIRAGDAFLSLGSSGVLFAATAHHAPNAQQGVHAFCHCLPGQWHQMSVILSAAASL 302

Query: 301 NWHSGVTGRSAAELTS-----ELGESLKAPGSVTFLPYLSGERTPHNDATIRGVFAGLGH 355
           +W SGVT R  AEL S       G+  +AP    FLPYL+GERTPHNDA  +GV  G+  
Sbjct: 303 HWLSGVTARPVAELVSGAERLSAGQQAQAP---LFLPYLNGERTPHNDAAAKGVLFGMTP 359

Query: 356 ESSRAVLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWLSSIATALNLPV 415
               A L  AV+EGV+FA+ D   AL+AAGT L+    +GGGSRS +W    ATAL +P+
Sbjct: 360 AHESAHLAYAVMEGVAFAMADGYAALQAAGTTLESAAFVGGGSRSAFWGVLCATALGIPL 419

Query: 416 DLPADGDFGAAFGAARLGLIAATGADPAAVCTAPETAETIAPEASLVPAYEDAYQRYRRL 475
              A  + GAA GAARLG +A TG D A+VC  PE  E   P+A+     +    +YRRL
Sbjct: 420 RRHAGAEVGAALGAARLGRLARTGEDAASVCIPPEVLEWYRPDAARQAQLQRRLAQYRRL 479

Query: 476 YPAIKE 481
           Y ++ +
Sbjct: 480 YRSLAD 485


Lambda     K      H
   0.317    0.132    0.401 

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: 655
Number of extensions: 35
Number of successful extensions: 3
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: 493
Length adjustment: 34
Effective length of query: 450
Effective length of database: 459
Effective search space:   206550
Effective search space used:   206550
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 HSERO_RS17030 HSERO_RS17030 (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.19110.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
     3e-171  556.1   0.0   3.4e-171  555.9   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS17030  HSERO_RS17030 xylulokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS17030  HSERO_RS17030 xylulokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  555.9   0.0  3.4e-171  3.4e-171       1     480 [.       4     480 ..       4     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 555.9 bits;  conditional E-value: 3.4e-171
                                  TIGR01312   1 lGiDlgTssvKallvdekgeviasgsasltvispkpgwsEqdpeewlealeealkellekakeekkei 68 
                                                lGiDlgTs+vK +l de  +vias+sa+l v +p+p wsEq p++w++a+ +a+++l+++a +  +++
  lcl|FitnessBrowser__HerbieS:HSERO_RS17030   4 LGIDLGTSEVKLVLTDEDSNVIASTSARLRVDNPHPLWSEQAPQSWWNATLDAIAALRTQAPQAFQAL 71 
                                                7******************************************************************* PP

                                  TIGR01312  69 kaisisGQmHglvlLDeegkvlrpaiLWnDtrtaeeceeleeelgeeelleltgnlalegfTapKllW 136
                                                ++i++sGQmHg++lLD +g+vlrpaiLWnD r+++ec ele+ ++   ++++tgn a++gfTapKllW
  lcl|FitnessBrowser__HerbieS:HSERO_RS17030  72 RGIGLSGQMHGATLLDRNGNVLRPAILWNDMRAHAECVELEALVP--DAVAITGNRAMPGFTAPKLLW 137
                                                ********************************************9..999****************** PP

                                  TIGR01312 137 vrkhepevfariakvlLPkDylrykLtgevvteysDAsGTllfdvkkrewskellkaldleesllPkl 204
                                                + k+ep v++ i+kvlLPkD+l +kLtge+v+e+sDA+GTl++dv++r+ws+ +l a+ l++s +P+l
  lcl|FitnessBrowser__HerbieS:HSERO_RS17030 138 LSKYEPAVYRAIDKVLLPKDFLGWKLTGEFVSEMSDAAGTLWLDVARRDWSERMLGATGLDRSHMPRL 205
                                                ******************************************************************** PP

                                  TIGR01312 205 vessekaGkvreevakklGleegvkvaaGggdnaagAiGlgivkegkvlvslGtSGvvlavedkaesd 272
                                                ve+s++aG++r+e+ +++G++  v va+G+gdnaa+A+G+g++++g++++slG+SGv++a++ ++ ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS17030 206 VEGSAVAGQLRDELRREWGISGPVVVAGGAGDNAASAVGIGVIRAGDAFLSLGSSGVLFAATAHHAPN 273
                                                ******************************************************************** PP

                                  TIGR01312 273 pegavhsFchalpgkwyplgvtlsatsalewlkellgeldveelneeaekvevg..aegvlllPylsG 338
                                                 ++ vh+Fch+lpg+w++++v+lsa+++l+wl+ +++   v+el+  ae+ ++g  a++ l+lPyl+G
  lcl|FitnessBrowser__HerbieS:HSERO_RS17030 274 AQQGVHAFCHCLPGQWHQMSVILSAAASLHWLSGVTA-RPVAELVSGAERLSAGqqAQAPLFLPYLNG 340
                                                *************************************.9**********9999877999********* PP

                                  TIGR01312 339 ERtPhldpqargsliGltanttradlarAvlegvafalrdsldilkelkglkikeirliGGGaksevw 406
                                                ERtPh+d++a+g+l+G+t +++ a+la+Av+egvafa++d+  +l++ +g+++++   +GGG++s++w
  lcl|FitnessBrowser__HerbieS:HSERO_RS17030 341 ERTPHNDAAAKGVLFGMTPAHESAHLAYAVMEGVAFAMADGYAALQA-AGTTLESAAFVGGGSRSAFW 407
                                                **********************************************9.67****************** PP

                                  TIGR01312 407 rqiladilglevvvpe.eeegaalGaAilAaialgekdlveecseavvkqkesvepiaenveayeely 473
                                                  + a+ lg +++ ++ +e gaalGaA+l+ +a + +d +++c    v ++ +  p+a+++++ ++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS17030 408 GVLCATALGIPLRRHAgAEVGAALGAARLGRLARTGEDAASVCIPPEVLEWYR--PDAARQAQLQRRL 473
                                                ***************98999***************999******999999988..************* PP

                                  TIGR01312 474 erykkly 480
                                                ++y++ly
  lcl|FitnessBrowser__HerbieS:HSERO_RS17030 474 AQYRRLY 480
                                                *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (481 nodes)
Target sequences:                          1  (493 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: 9.08
//
[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