Alignments for a candidate for xylA in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Stenotrophomonas chelatiphaga DSM 21508

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate WP_057508164.1 ABB28_RS08200 xylose isomerase

Query= reanno::Cola:Echvi_1876
         (437 letters)



>NCBI__GCF_001431535.1:WP_057508164.1
          Length = 446

 Score =  582 bits (1500), Expect = e-171
 Identities = 273/435 (62%), Positives = 333/435 (76%)

Query: 3   KTYFPGIEKIKYEGRDSKNPFAFKFYDENKVVAGKTMKEHFKFAIAYWHSFNATGDDPFG 62
           + +FPG+ +I +EGRDS NP A+K YD +K + G++M EH +FA+AYWHSF   G DPFG
Sbjct: 10  REFFPGVGRIPFEGRDSDNPLAYKVYDADKQIGGRSMAEHLRFAVAYWHSFCGAGHDPFG 69

Query: 63  PGTKTFVWDQAEDALQRAKDKMDAAFEFITKIGAPYYCFHDVDLIDEGSTIEEYESRMKA 122
           PGT+ + WDQ    L RA+ K DAAFEF+TK+G PYYCFHDVDL  +   I EY + +  
Sbjct: 70  PGTRVYPWDQGATPLARAEAKADAAFEFVTKLGVPYYCFHDVDLAPDADDIGEYRANLGH 129

Query: 123 ITEYAKQKQVETGVKLLWGTANVFSNPRYMNGASTNPDFDVVSWAATQVKNSIDATIALG 182
           + E A ++Q +TGVKLLWGTAN+FS+PRYMNGA+TNPDF VV+ AA QV+ ++DAT+ALG
Sbjct: 130 MVEIAGERQRQTGVKLLWGTANLFSHPRYMNGAATNPDFAVVARAAVQVRAALDATVALG 189

Query: 183 GENYVFWGGREGYMSLLNTDMKRETEHLAKFLTMARDYGRKQGFKGNFLIEPKPMEPTKH 242
           G NYVFWGGREGY  LLNTDMKRE  HLA+FL  ARDYGR  GF G FLIEPKPMEP  H
Sbjct: 190 GSNYVFWGGREGYACLLNTDMKREQAHLARFLAAARDYGRSIGFTGTFLIEPKPMEPMHH 249

Query: 243 QYDYDSATVVGFLRHYGLDKDFKLNIEVNHATLAGHTFQHELQVAADAGLLGSIDANRGD 302
           QYD+DSATVVGFLR +GLD+DFKLNIE NHATL+GHTF H+LQVA+DAGLLGSIDANRG+
Sbjct: 250 QYDFDSATVVGFLRAHGLDRDFKLNIEANHATLSGHTFAHDLQVASDAGLLGSIDANRGN 309

Query: 303 YQNGWDTDQFALNLQELTESLLVILEAGGLQGGGVNFDAKLRRNSTDLDDLFHAHIGSMD 362
            QNGWDTDQF  +L +   ++LV+L  GG   GG+NFDAK+RR S+D  DLF AHIG MD
Sbjct: 310 PQNGWDTDQFPTDLYDAVGAMLVVLRQGGFGDGGLNFDAKVRRESSDPQDLFIAHIGGMD 369

Query: 363 AFARALLIANDILEQSEYKALRKKRYASFDGGKGKEFEEGKLTLEDLREHAIATGEPAST 422
            FAR L +A+ ++  S  +  R +RYASFD G G  F  G+LTL+DL  HA   GEP   
Sbjct: 370 TFARGLEVAHALVTASPLEQWRSERYASFDSGAGAAFANGQLTLQDLCAHAQQAGEPRQR 429

Query: 423 SGKQEMYENIINQYI 437
           SG+QE YEN++NQY+
Sbjct: 430 SGRQEAYENLLNQYL 444


Lambda     K      H
   0.317    0.135    0.400 

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: 665
Number of extensions: 21
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: 437
Length of database: 446
Length adjustment: 32
Effective length of query: 405
Effective length of database: 414
Effective search space:   167670
Effective search space used:   167670
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate WP_057508164.1 ABB28_RS08200 (xylose isomerase)
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.21005.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.6e-209  682.2   0.0   1.8e-209  682.0   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057508164.1  ABB28_RS08200 xylose isomerase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057508164.1  ABB28_RS08200 xylose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  682.0   0.0  1.8e-209  1.8e-209       1     435 []      12     444 ..      12     444 .. 0.99

  Alignments for each domain:
  == domain 1  score: 682.0 bits;  conditional E-value: 1.8e-209
                                 TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpwdke 69 
                                               ff+++ ++ +eG+ds+npla+k+y++++ i g++m +hlrfavayWh+++  g+DpfG gt  +pwd+ 
  lcl|NCBI__GCF_001431535.1:WP_057508164.1  12 FFPGVGRIPFEGRDSDNPLAYKVYDADKQIGGRSMAEHLRFAVAYWHSFCGAGHDPFGPGTRVYPWDQ- 79 
                                               89*****************************************************************6. PP

                                 TIGR02630  70 ltdaldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketgvklLWg 138
                                                +++l++a+ak+daafe+++klgv+yycfhDvD+ap+++++ e+ anl ++v+++ e+q++tgvklLWg
  lcl|NCBI__GCF_001431535.1:WP_057508164.1  80 GATPLARAEAKADAAFEFVTKLGVPYYCFHDVDLAPDADDIGEYRANLGHMVEIAGERQRQTGVKLLWG 148
                                               69******************************************************************* PP

                                 TIGR02630 139 tanlfshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlntdlkleldnl 207
                                               tanlfshpry++Gaat+pd+ v+a+aa+qv++al++t  lgg nyvfWGGreGy +Llntd+k+e+ +l
  lcl|NCBI__GCF_001431535.1:WP_057508164.1 149 TANLFSHPRYMNGAATNPDFAVVARAAVQVRAALDATVALGGSNYVFWGGREGYACLLNTDMKREQAHL 217
                                               ********************************************************************* PP

                                 TIGR02630 208 arflklavdyakkigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfklnieanhatLaght 276
                                               arfl  a+dy ++igf+g++liePkP+eP++hqyDfD+atv++fl++++Ld+dfklnieanhatL+ght
  lcl|NCBI__GCF_001431535.1:WP_057508164.1 218 ARFLAAARDYGRSIGFTGTFLIEPKPMEPMHHQYDFDSATVVGFLRAHGLDRDFKLNIEANHATLSGHT 286
                                               ********************************************************************* PP

                                 TIGR02630 277 fehelrvarelgllGsiDanrgdlllGWDtDefptdvyeatlamyevlkagglakGGlnfdakvrresl 345
                                               f+h+l+va+++gllGsiDanrg+ ++GWDtD+fptd+y+a+ am+ vl++gg++ GGlnfdakvrres 
  lcl|NCBI__GCF_001431535.1:WP_057508164.1 287 FAHDLQVASDAGLLGSIDANRGNPQNGWDTDQFPTDLYDAVGAMLVVLRQGGFGDGGLNFDAKVRRESS 355
                                               ********************************************************************* PP

                                 TIGR02630 346 daeDlllahiagmDafarglkvaaklledgaleklveeryesfdseiGkeieegkadleelekyaleke 414
                                               d++Dl++ahi+gmD+fargl+va +l++++ le++ +ery+sfds++G+++++g+ +l++l ++a++ +
  lcl|NCBI__GCF_001431535.1:WP_057508164.1 356 DPQDLFIAHIGGMDTFARGLEVAHALVTASPLEQWRSERYASFDSGAGAAFANGQLTLQDLCAHAQQAG 424
                                               ********************************************************************9 PP

                                 TIGR02630 415 eeaekksgrqelleslinkyl 435
                                               e ++++sgrqe++e+l+n+yl
  lcl|NCBI__GCF_001431535.1:WP_057508164.1 425 E-PRQRSGRQEAYENLLNQYL 444
                                               7.*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (446 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: 9.44
//
[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 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