Alignments for a candidate for xylA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylA in Dyella japonica UNC79MFTsu3.2

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate N515DRAFT_3229 N515DRAFT_3229 D-xylose isomerase (EC 5.3.1.5)

Query= reanno::BFirm:BPHYT_RS32825
         (440 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3229
          Length = 438

 Score =  680 bits (1755), Expect = 0.0
 Identities = 313/437 (71%), Positives = 372/437 (85%)

Query: 1   MSYFEHIPEIRYEGPQSDNPLAYRHYDKSKKVLGKTLEEHLRIAVCYWHTFVWPGVDIFG 60
           MSYFEH+  IRY G ++D+PLA+RHYD S+ +LGK ++EHLR+AVCYWH+FVWPG+D+FG
Sbjct: 1   MSYFEHVAPIRYAGAKTDDPLAFRHYDPSRVILGKRMDEHLRLAVCYWHSFVWPGMDMFG 60

Query: 61  QGTFRRPWQQAGDAMERAQQKADSAFEFFSKLGTPYYTFHDTDVSPEGSNLKEYSENFLR 120
            GTF+RPWQQAGD M +A  KAD+AF+FF +LG P+YTFHDTDV+PEG+NL EYS NF  
Sbjct: 61  AGTFQRPWQQAGDLMAQAHAKADAAFDFFQRLGAPFYTFHDTDVAPEGANLAEYSRNFAA 120

Query: 121 ITDYLARKQESTGIKLLWGTANLFSHPRYAAGAATSPDPEVFAFAATQVRHALDATQRLG 180
           + D L  KQ  TG+KLLWGTANLFSHPRYAAGAA+SP PEVFA+AA+QV HA+ AT RLG
Sbjct: 121 MVDVLEAKQAQTGMKLLWGTANLFSHPRYAAGAASSPQPEVFAYAASQVFHAMGATHRLG 180

Query: 181 GDNYVLWGGREGYDTLLNTDLVRERDQLARFLHMVVDHAHKIGFKGSLLIEPKPQEPTKH 240
           G NYVLWGGREGYDTLLNTDL RER QL RF  MVV+H HK+GF+G++LIEPKPQEPTKH
Sbjct: 181 GANYVLWGGREGYDTLLNTDLRRERAQLGRFFQMVVEHKHKLGFQGTILIEPKPQEPTKH 240

Query: 241 QYDYDVATVHGFLLQHGLDKEIRVNIEANHATLAGHSFHHEIATAYALGIFGSVDANRGD 300
           QYDYD ATV+GFL + GL++E++VN+EANHATLAGHSFHHE+ATA +LG+FGS+DANRGD
Sbjct: 241 QYDYDTATVYGFLKEFGLEREVKVNLEANHATLAGHSFHHEVATAISLGVFGSIDANRGD 300

Query: 301 PQNGWDTDQFPNSVEELTLAFYEILKHGGFTTGGMNFDSKVRRQSVDPEDLFYGHIGAID 360
           PQNGWDTDQFPNSVEELTL  YEIL+ GGFTTGG NFD+KVRRQSVD  DLF+GH+GAID
Sbjct: 301 PQNGWDTDQFPNSVEELTLVMYEILQAGGFTTGGFNFDTKVRRQSVDAADLFHGHVGAID 360

Query: 361 NLALAVERAAVLIENDRLDQFKRQRYSGWDAEFGRKISSGDYSLSALAEEAMARGLNPQH 420
            LALA+ERAA +I++DRL  FK QRY+GWDA  G++I  G Y+L ALA+EA  R L P H
Sbjct: 361 ALALALERAAKMIDDDRLAAFKAQRYAGWDAGLGQQILDGGYTLQALADEAAKRDLRPGH 420

Query: 421 ASGHQELMENIVNQAIY 437
            SG QE +EN+VN+ IY
Sbjct: 421 VSGQQERLENLVNRYIY 437


Lambda     K      H
   0.319    0.136    0.414 

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: 755
Number of extensions: 20
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: 440
Length of database: 438
Length adjustment: 32
Effective length of query: 408
Effective length of database: 406
Effective search space:   165648
Effective search space used:   165648
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate N515DRAFT_3229 N515DRAFT_3229 (D-xylose isomerase (EC 5.3.1.5))
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.16455.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.5e-204  665.8   0.3   1.7e-204  665.6   0.3    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_3229  N515DRAFT_3229 D-xylose isomeras


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_3229  N515DRAFT_3229 D-xylose isomerase (EC 5.3.1.5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  665.6   0.3  1.7e-204  1.7e-204       1     435 []       3     436 ..       3     436 .. 1.00

  Alignments for each domain:
  == domain 1  score: 665.6 bits;  conditional E-value: 1.7e-204
                                    TIGR02630   1 ffeeiekvkyeGkdsknplafkyynpeeviegkkmkdhlrfavayWhtlaaegaDpfGagtaerpw 66 
                                                  +fe+++ ++y+G ++++plaf++y+p +vi gk+m +hlr av+yWh++ + g D+fGagt++rpw
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3229   3 YFEHVAPIRYAGAKTDDPLAFRHYDPSRVILGKRMDEHLRLAVCYWHSFVWPGMDMFGAGTFQRPW 68 
                                                  8***************************************************************** PP

                                    TIGR02630  67 dkeltdaldkakakvdaafelleklgveyycfhDvDiapegaslketnanldeivdllkekqketg 132
                                                  ++   d +++a+ak+daaf+++++lg+++y+fhD+D+apega+l+e+++n+ ++vd+l+ kq++tg
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3229  69 QQ-AGDLMAQAHAKADAAFDFFQRLGAPFYTFHDTDVAPEGANLAEYSRNFAAMVDVLEAKQAQTG 133
                                                  96.69************************************************************* PP

                                    TIGR02630 133 vklLWgtanlfshpryvaGaatspdadvfayaaaqvkkalevtkklggenyvfWGGreGyetLlnt 198
                                                  +klLWgtanlfshpry+aGaa sp+++vfayaa+qv +a+ +t++lgg nyv+WGGreGy+tLlnt
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 134 MKLLWGTANLFSHPRYAAGAASSPQPEVFAYAASQVFHAMGATHRLGGANYVLWGGREGYDTLLNT 199
                                                  ****************************************************************** PP

                                    TIGR02630 199 dlkleldnlarflklavdyakkigfkgqlliePkPkePtkhqyDfDaatvlaflkkydLdkdfkln 264
                                                  dl++e+ +l+rf++++v++++k+gf+g++liePkP+ePtkhqyD+D+atv++flk+++L++++k+n
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 200 DLRRERAQLGRFFQMVVEHKHKLGFQGTILIEPKPQEPTKHQYDYDTATVYGFLKEFGLEREVKVN 265
                                                  ****************************************************************** PP

                                    TIGR02630 265 ieanhatLaghtfehelrvarelgllGsiDanrgdlllGWDtDefptdvyeatlamyevlkaggla 330
                                                  +eanhatLagh+f+he+++a +lg++GsiDanrgd ++GWDtD+fp++v+e+tl+mye+l+agg++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 266 LEANHATLAGHSFHHEVATAISLGVFGSIDANRGDPQNGWDTDQFPNSVEELTLVMYEILQAGGFT 331
                                                  ****************************************************************** PP

                                    TIGR02630 331 kGGlnfdakvrresldaeDlllahiagmDafarglkvaaklledgaleklveeryesfdseiGkei 396
                                                  +GG+nfd kvrr+s+da Dl+++h++++Da+a++l+ aak+++d++l ++ ++ry+++d ++G++i
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 332 TGGFNFDTKVRRQSVDAADLFHGHVGAIDALALALERAAKMIDDDRLAAFKAQRYAGWDAGLGQQI 397
                                                  ****************************************************************** PP

                                    TIGR02630 397 eegkadleelekyalekeeeaekksgrqelleslinkyl 435
                                                  ++g  +l+ l+++a++++ ++ + sg+qe le+l+n+y+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_3229 398 LDGGYTLQALADEAAKRDLRPGHVSGQQERLENLVNRYI 436
                                                  *************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (435 nodes)
Target sequences:                          1  (438 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: 00:00:00.01
# Mc/sec: 9.83
//
[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