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

GapMind for catabolism of small carbon sources

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

Align ABC transporter related (characterized, see rationale)
to candidate WP_022528026.1 L248_RS00360 sugar ABC transporter ATP-binding protein

Query= uniprot:A0KWY5
         (499 letters)



>NCBI__GCF_000469325.1:WP_022528026.1
          Length = 515

 Score =  281 bits (718), Expect = 5e-80
 Identities = 158/474 (33%), Positives = 279/474 (58%), Gaps = 9/474 (1%)

Query: 3   LILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDIL 62
           ++L ++ +SK +   + L+ + + +  G V  L+GENGAGKST++K + G +++D G   
Sbjct: 21  VMLSIRGLSKSFGRNRVLDHIDMDVKKGSVMGLMGENGAGKSTMMKCLFGIKTRDEGKFY 80

Query: 63  FLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLG-YEPRRLGLIHFKKMYADA 121
             G+   F  P DA + GI+ V+QE+N   + +V  NLFLG Y    LG++  ++M  +A
Sbjct: 81  LDGKEVSFQGPKDALENGIAMVHQELNQALDRSVVDNLFLGRYPVNALGVVDERQMRREA 140

Query: 122 RAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFG 181
             +  +  + ++++ P+   S++ +Q++ IA+ ++  +KV+VLDEPT+SL A+EV  LF 
Sbjct: 141 TELFRRLGMTVNLTQPMRKMSVSQRQMVEIAKAISYHSKVIVLDEPTSSLMAQEVDKLFD 200

Query: 182 ILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSL 241
           ++  LK +G++I+FI+H +D+V+QI D ++VLR+G  +    TA+    +L++AM+GR L
Sbjct: 201 MVRMLKKQGISIIFISHKMDEVFQICDEVSVLRDGHLVMTKKTADTNMNELVKAMVGRPL 260

Query: 242 QEQLVDKQEKERTVTRAEAVLLSLEDVSVKGS--IQSMNLTVPKGQAVGLAGLLGSGRSE 299
             +       +  V +    +L +  +S K S  +Q +  +V +G+  GL GL+G+GR+E
Sbjct: 261 DNRF---PPVDNVVGK---TILQVSHLSTKFSPYLQDITFSVGQGEIFGLYGLVGAGRTE 314

Query: 300 VCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIIL 359
           +   +FG+    +G ++  G+  N +   +A+  G A+  E+RK +G+    S+  N  +
Sbjct: 315 LLETIFGVRTRAAGRVYFNGKLANFNSAKEAMDHGFAMITEERKANGLFLKGSLTFNTTI 374

Query: 360 ALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEP 419
                      LS  +  +     I  +   T   D+ I  LSGGNQQKVI+ +WL   P
Sbjct: 375 TNLDAYKRGVALSEQKMTKATLKEIQVMNTKTMGPDELIASLSGGNQQKVIIGKWLERLP 434

Query: 420 ILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473
            L ++DEPTRGID+GA  EI +LI  +  +G +++V SSE+ E++  +N++ V+
Sbjct: 435 QLFMMDEPTRGIDVGAKYEIYELIIQMAKQGKTIIVVSSEMPEILGITNRIGVM 488



 Score = 80.5 bits (197), Expect = 1e-19
 Identities = 62/262 (23%), Positives = 127/262 (48%), Gaps = 13/262 (4%)

Query: 241 LQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGS----IQSMNLTVPKGQAVGLAGLLGSG 296
           +QE  V    K +       V+LS+  +S        +  +++ V KG  +GL G  G+G
Sbjct: 1   MQEAPVLNVNKSQEPPVDSDVMLSIRGLSKSFGRNRVLDHIDMDVKKGSVMGLMGENGAG 60

Query: 297 RSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPED--RKIDGIIGPLSIR 354
           +S +   +FG+   D G  +L G++++   P DA+  GIA+  ++  + +D      S+ 
Sbjct: 61  KSTMMKCLFGIKTRDEGKFYLDGKEVSFQGPKDALENGIAMVHQELNQALDR-----SVV 115

Query: 355 ENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARW 414
           +N+ L                ++E  + F  +    T +  +P+ ++S   +Q V +A+ 
Sbjct: 116 DNLFLGRYPVNALGVVDERQMRREATELF--RRLGMTVNLTQPMRKMSVSQRQMVEIAKA 173

Query: 415 LAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLR 474
           ++    ++VLDEPT  +      ++  ++R L  +G+S++  S ++DE+    ++V VLR
Sbjct: 174 ISYHSKVIVLDEPTSSLMAQEVDKLFDMVRMLKKQGISIIFISHKMDEVFQICDEVSVLR 233

Query: 475 DRYAVRELSGAELTSQHVMQAI 496
           D + V     A+     +++A+
Sbjct: 234 DGHLVMTKKTADTNMNELVKAM 255



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 52/239 (21%), Positives = 112/239 (46%), Gaps = 14/239 (5%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           IL++  +S  +     L+D++  +  GE+  L G  GAG++ L++ + G +++  G + F
Sbjct: 275 ILQVSHLSTKFSPY--LQDITFSVGQGEIFGLYGLVGAGRTELLETIFGVRTRAAGRVYF 332

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEV---------NLVPNLTVAQNLFLGYEPRRLGLIHF 114
            G+  +FN+  +A   G + + +E          +L  N T+     L    R + L   
Sbjct: 333 NGKLANFNSAKEAMDHGFAMITEERKANGLFLKGSLTFNTTITN---LDAYKRGVALSEQ 389

Query: 115 KKMYADARAVLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAK 174
           K   A  + +       +     ++  S   QQ + I + +    ++ ++DEPT  +D  
Sbjct: 390 KMTKATLKEIQVMNTKTMGPDELIASLSGGNQQKVIIGKWLERLPQLFMMDEPTRGIDVG 449

Query: 175 EVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLI 233
               ++ ++ Q+  +G  I+ ++  + ++  I++RI V+ NG+  G   T +  Q +L+
Sbjct: 450 AKYEIYELIIQMAKQGKTIIVVSSEMPEILGITNRIGVMSNGRLAGIVNTKQTNQEELL 508


Lambda     K      H
   0.319    0.136    0.377 

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: 543
Number of extensions: 28
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: 499
Length of database: 515
Length adjustment: 34
Effective length of query: 465
Effective length of database: 481
Effective search space:   223665
Effective search space used:   223665
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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