Alignments for a candidate for xylA in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Dinoroseobacter shibae DFL-12

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate 3608603 Dshi_1996 xylose isomerase (RefSeq)

Query= reanno::Smeli:SMc03163
         (436 letters)



>FitnessBrowser__Dino:3608603
          Length = 434

 Score =  646 bits (1667), Expect = 0.0
 Identities = 299/432 (69%), Positives = 357/432 (82%), Gaps = 1/432 (0%)

Query: 5   FFGDIAKIKYEGPESTNPLAFRHYNPDDVVLGKRMEDHLRFAVAYWHTFVWPGGDPFGGQ 64
           FF  I  + YEGPE+ +  AFRHYNPD++V+GKRMED LRFAVA+WH+F W GGDPFGG 
Sbjct: 4   FFAGIPAVTYEGPEARSDFAFRHYNPDEMVMGKRMEDQLRFAVAWWHSFAWEGGDPFGGP 63

Query: 65  TFERPWFKDSMEAAKLKADVAFEFFQLLGVPYYCFHDADVRPEGRNFAENTSNLNAIVDY 124
           TF+RPWF D+++ A+ KAD AFE F++L VP+YCFHDAD+RPEG +FAE T+NL A+VDY
Sbjct: 64  TFQRPWFGDTLDHARAKADAAFEMFRILNVPFYCFHDADIRPEGASFAETTANLEAMVDY 123

Query: 125 FAGKQGETGVKLLWGTANLFSNRRFMAGAATNPDPDVFAFAAATVKTCIDATQRLDGENY 184
              KQ  +G +LLWGTANLFS+RR+MAGAATNPDPDVFA+AAAT+KTC+DAT +L G NY
Sbjct: 124 LGQKQEASGKRLLWGTANLFSHRRYMAGAATNPDPDVFAYAAATIKTCMDATHKLGGANY 183

Query: 185 VLWGGREGYETLLNTDLKRELDQLGRFLNLVVEYKHRIGFKGTILIEPKPQEPTKHQYDY 244
           VLWGGREGYETLLNTDL RE +Q GR L +VV+YKH+IGF+GTIL+EPKPQEPTKHQYDY
Sbjct: 184 VLWGGREGYETLLNTDLGREREQAGRMLQMVVDYKHKIGFEGTILLEPKPQEPTKHQYDY 243

Query: 245 DVATVYGFLKRYGLENEVKVNIEQGHAILAGHSFEHELALANALGIFGSIDMNRNDYQSG 304
           DVATV+ FL  +GL++EVK+NIEQGHAILAGHSFEHELALA   GI GSIDMNRNDYQSG
Sbjct: 244 DVATVFSFLSEFGLQDEVKMNIEQGHAILAGHSFEHELALAREFGILGSIDMNRNDYQSG 303

Query: 305 WDTDQFPNNVPEMALAYYHVLAGGGFKTGGTNFDAKLRRQSIDPEDLLIGHIGGMDCCAR 364
           WDTDQFPNN+PE+ALAYY +L  GGF TGGTNFD+KLRRQS+DP DL+  H+  MD CA 
Sbjct: 304 WDTDQFPNNIPEVALAYYEILRAGGFDTGGTNFDSKLRRQSLDPADLIAAHVAAMDVCAA 363

Query: 365 GLKAAAKMIEDKALSAPLEARYAGWNVPEAKKMLDGGFSLEEIEAWVLKSDVNPQPKSGR 424
           GLKAAA+M+ED  L    E RYAGW  P A+ ML+GG  LE+  A V+++ ++PQP SG 
Sbjct: 364 GLKAAARMLEDGELEQRREDRYAGWRAPSAEAMLNGG-KLEDCFAHVMETGLDPQPVSGG 422

Query: 425 QELLENVVNRYV 436
           QE LE +V RY+
Sbjct: 423 QERLEALVARYL 434


Lambda     K      H
   0.320    0.139    0.429 

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: 764
Number of extensions: 26
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: 436
Length of database: 434
Length adjustment: 32
Effective length of query: 404
Effective length of database: 402
Effective search space:   162408
Effective search space used:   162408
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: 51 (24.3 bits)

Align candidate 3608603 Dshi_1996 (xylose isomerase (RefSeq))
to HMM TIGR02630 (xylA: xylose isomerase (EC 5.3.1.5))

# 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/TIGR02630.hmm
# target sequence database:        /tmp/gapView.7668.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02630  [M=435]
Accession:   TIGR02630
Description: xylose_isom_A: xylose isomerase
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-201  655.7   0.0     2e-201  655.5   0.0    1.0  1  lcl|FitnessBrowser__Dino:3608603  Dshi_1996 xylose isomerase (RefS


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608603  Dshi_1996 xylose isomerase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  655.5   0.0    2e-201    2e-201       1     435 []       4     434 .]       4     434 .] 0.99

  Alignments for each domain:
  == domain 1  score: 655.5 bits;  conditional E-value: 2e-201
                         TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdkeltdaldka 77 
                                       ff +i  v+yeG+++++ +af++ynp+e+++gk+m+d+lrfava+Wh++a+eg+DpfG+ t++rpw     d+ld+a
  lcl|FitnessBrowser__Dino:3608603   4 FFAGIPAVTYEGPEARSDFAFRHYNPDEMVMGKRMEDQLRFAVAWWHSFAWEGGDPFGGPTFQRPWF---GDTLDHA 77 
                                       899***************************************************************9...589**** PP

                         TIGR02630  78 kakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWgtanlfshpryvaGaat 154
                                       +ak+daafe+++ l+v++ycfhD+Di pegas++et+anl+++vd+l +kq+++g +lLWgtanlfsh+ry+aGaat
  lcl|FitnessBrowser__Dino:3608603  78 RAKADAAFEMFRILNVPFYCFHDADIRPEGASFAETTANLEAMVDYLGQKQEASGKRLLWGTANLFSHRRYMAGAAT 154
                                       ***************************************************************************** PP

                         TIGR02630 155 spdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnlarflklavdyakkigfkgqllieP 231
                                       +pd+dvfayaaa++k+++++t+klgg nyv+WGGreGyetLlntdl +e+++ +r+l+++vdy++kigf+g++l+eP
  lcl|FitnessBrowser__Dino:3608603 155 NPDPDVFAYAAATIKTCMDATHKLGGANYVLWGGREGYETLLNTDLGREREQAGRMLQMVVDYKHKIGFEGTILLEP 231
                                       ***************************************************************************** PP

                         TIGR02630 232 kPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaghtfehelrvarelgllGsiDanrgdlllGWDtDe 308
                                       kP+ePtkhqyD+D+atv++fl +++L++++k+nie+ ha+Lagh+fehel++are g+lGsiD+nr+d++ GWDtD+
  lcl|FitnessBrowser__Dino:3608603 232 KPQEPTKHQYDYDVATVFSFLSEFGLQDEVKMNIEQGHAILAGHSFEHELALAREFGILGSIDMNRNDYQSGWDTDQ 308
                                       ***************************************************************************** PP

                         TIGR02630 309 fptdvyeatlamyevlkagglakGGlnfdakvrresldaeDlllahiagmDafarglkvaaklledgaleklveery 385
                                       fp+++ e++la+ye+l+agg+++GG+nfd+k+rr+sld+ Dl+ ah+a+mD +a+glk+aa++ledg+le+  e+ry
  lcl|FitnessBrowser__Dino:3608603 309 FPNNIPEVALAYYEILRAGGFDTGGTNFDSKLRRQSLDPADLIAAHVAAMDVCAAGLKAAARMLEDGELEQRREDRY 385
                                       ***************************************************************************** PP

                         TIGR02630 386 esfdseiGkeieegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                       ++++    +++++g  +le+  ++++e++ +++  sg qe le+l+ +yl
  lcl|FitnessBrowser__Dino:3608603 386 AGWRAPSAEAMLNG-GKLEDCFAHVMETGLDPQPVSGGQERLEALVARYL 434
                                       ***********999.78*****************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (434 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: 7.30
//
[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