Alignments for a candidate for ytfR in Lactobacillus shenzhenensis LY-73

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Lactobacillus shenzhenensis LY-73

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_022528026.1 L248_RS00360 sugar ABC transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>NCBI__GCF_000469325.1:WP_022528026.1
          Length = 515

 Score =  324 bits (831), Expect = 4e-93
 Identities = 180/473 (38%), Positives = 284/473 (60%), Gaps = 12/473 (2%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L   GLSK F   + LD++D  +++G +M L+GENGAGKST++K L G+   D G  +L
Sbjct: 22  MLSIRGLSKSFGRNRVLDHIDMDVKKGSVMGLMGENGAGKSTMMKCLFGIKTRDEGKFYL 81

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREP-KRFGLLRRKEMEKRAT 127
           +G+ +S +    A + GI  V+QE+N   + SV DNLF+GR P    G++  ++M + AT
Sbjct: 82  DGKEVSFQGPKDALENGIAMVHQELNQALDRSVVDNLFLGRYPVNALGVVDERQMRREAT 141

Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187
           EL    G ++++ +P+ + SV+ +Q+V I +AI   +KV++LDEPT+SL  QEV+ LFD+
Sbjct: 142 ELFRRLGMTVNLTQPMRKMSVSQRQMVEIAKAISYHSKVIVLDEPTSSLMAQEVDKLFDM 201

Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247
           +R L+ +G+S+IF++H +D+V+Q+ D ++VLR+G  V  ++T +    ELVK M+GR LD
Sbjct: 202 VRMLKKQGISIIFISHKMDEVFQICDEVSVLRDGHLVMTKKTADTNMNELVKAMVGRPLD 261

Query: 248 TH---ALQRAGRTLLSDKPVAA-FKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303
                     G+T+L    ++  F  Y     +      V  GEI GL GL+G+GRTE  
Sbjct: 262 NRFPPVDNVVGKTILQVSHLSTKFSPY-----LQDITFSVGQGEIFGLYGLVGAGRTELL 316

Query: 304 EVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVREN-IILA 362
           E IFG++   +G     GK  N  S  +A   G     E+RK +G+    S+  N  I  
Sbjct: 317 ETIFGVRTRAAGRVYFNGKLANFNSAKEAMDHGFAMITEERKANGLFLKGSLTFNTTITN 376

Query: 363 LQAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQ 422
           L A +  +  +S ++  +   + I+ +  +T   ++ I  LSGGNQQKV++ +WL   PQ
Sbjct: 377 LDAYKRGV-ALSEQKMTKATLKEIQVMNTKTMGPDELIASLSGGNQQKVIIGKWLERLPQ 435

Query: 423 FLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475
             ++DEPTRGIDVGA  EI  LI  +   G  ++V+SSE+ E++G  +R+ +M
Sbjct: 436 LFMMDEPTRGIDVGAKYEIYELIIQMAKQGKTIIVVSSEMPEILGITNRIGVM 488



 Score = 84.3 bits (207), Expect = 9e-21
 Identities = 54/231 (23%), Positives = 113/231 (48%), Gaps = 5/231 (2%)

Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327
           K++G+   +   D++V+ G ++GL G  G+G++   + +FGIK  D G   + GK  + +
Sbjct: 30  KSFGRNRVLDHIDMDVKKGSVMGLMGENGAGKSTMMKCLFGIKTRDEGKFYLDGKEVSFQ 89

Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIR 387
            P  A   GI    ++          SV +N+ L        L  +  ++ +  A    R
Sbjct: 90  GPKDALENGIAMVHQELNQ---ALDRSVVDNLFLGRYPVNA-LGVVDERQMRREATELFR 145

Query: 388 QLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIET 447
           +LG+ T +  QP+  +S   +Q V +++ +    + ++LDEPT  +      ++  ++  
Sbjct: 146 RLGM-TVNLTQPMRKMSVSQRQMVEIAKAISYHSKVIVLDEPTSSLMAQEVDKLFDMVRM 204

Query: 448 LCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAIMNAI 498
           L   G++++ IS +++E+    D V ++RD   V     A+ ++  ++ A+
Sbjct: 205 LKKQGISIIFISHKMDEVFQICDEVSVLRDGHLVMTKKTADTNMNELVKAM 255



 Score = 71.2 bits (173), Expect = 8e-17
 Identities = 57/239 (23%), Positives = 113/239 (47%), Gaps = 10/239 (4%)

Query: 9   ILRTEGLS-KFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIW 67
           IL+   LS KF P    L ++ FS+ +GEI  L G  GAG++ L++ + GV     G ++
Sbjct: 275 ILQVSHLSTKFSP---YLQDITFSVGQGEIFGLYGLVGAGRTELLETIFGVRTRAAGRVY 331

Query: 68  LEGQAISPKNTAHAQQLGIGTVYQEVN----LLPNMSVADNLFIGREPKRFGLLRRKEME 123
             G+  +  +   A   G   + +E       L      +      +  + G+   ++  
Sbjct: 332 FNGKLANFNSAKEAMDHGFAMITEERKANGLFLKGSLTFNTTITNLDAYKRGVALSEQKM 391

Query: 124 KRAT--ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEV 181
            +AT  E+      ++   E +   S   QQ V I + ++   ++ ++DEPT  +D    
Sbjct: 392 TKATLKEIQVMNTKTMGPDELIASLSGGNQQKVIIGKWLERLPQLFMMDEPTRGIDVGAK 451

Query: 182 ELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKM 240
             +++L+ Q+  +G ++I V+  + ++  +++RI V+ NG   G   T +  Q EL+++
Sbjct: 452 YEIYELIIQMAKQGKTIIVVSSEMPEILGITNRIGVMSNGRLAGIVNTKQTNQEELLRL 510


Lambda     K      H
   0.321    0.138    0.391 

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: 572
Number of extensions: 31
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 500
Length of database: 515
Length adjustment: 34
Effective length of query: 466
Effective length of database: 481
Effective search space:   224146
Effective search space used:   224146
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)

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 2024 update 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