GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS16930 in Lactobacillus shenzhenensis LY-73

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate WP_022530418.1 L248_RS11555 sugar ABC transporter ATP-binding protein

Query= uniprot:B2SYR5
         (512 letters)



>NCBI__GCF_000469325.1:WP_022530418.1
          Length = 508

 Score =  337 bits (864), Expect = 6e-97
 Identities = 189/494 (38%), Positives = 294/494 (59%), Gaps = 12/494 (2%)

Query: 5   LRFDNIGKVFPGVRALDGVSFDVNVGQVHGLMGENGAGKSTLLKILGGEYQPDSGRVMID 64
           L   +I K FPGV+ALD V  D+  G+VH LMGENGAGKSTL+K++ G Y+  SG V + 
Sbjct: 14  LSMRHIAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVTLH 73

Query: 65  GNEVRFTSAASSIAAGIAVIHQELQYVPDLTVAENLLLGQLPNSLGWVNKREAKRFVRER 124
           G ++   +   +   GI+ ++QE+   P+L+VAEN+ +G+ P   G ++         + 
Sbjct: 74  GQDINPKTPQEAQDLGISTVYQEVNLCPNLSVAENVYIGRQPMRFGQIDWHRMNADAVKL 133

Query: 125 LEAMGVALDPNAKLRKLSIAQRQMVEICKALLRNARVIALDEPTSSLSHRETEVLFKLVR 184
           LE++ + +D    L   S++ +QM+ I +A+  +A V+ LDEPTSSL   E   LF ++R
Sbjct: 134 LESLDIHVDVTKTLDSYSVSVQQMIAIARAVDMSAGVLILDEPTSSLDSNEVAQLFAIIR 193

Query: 185 DLRADNRAMIYISHRMDEIYELCDACTIFRDGRKIASHPTLEGVTRDTIVSEMVGREISD 244
            LR  N A+++++H MD++Y + D  T+ R+GR I  +   +    D +V++M+G++  D
Sbjct: 194 HLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELD-LVTKMIGQKFVD 252

Query: 245 IYNYSARP---LGEVRFA-AKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVY 300
               + RP      VRF   + I    L    S  VR GE++G  GL+G+GR+E+  L++
Sbjct: 253 ANTQAHRPSKDYSTVRFVRMEDISKRGLVHDFSMAVRAGEVLGLAGLLGSGRTEVAELLF 312

Query: 301 GADHKKGGELLLDGKPIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINIS--CRR 358
           G  H   G + +    +K  +  +A+   +  C EDRK  GIV   ++ ENI +S   ++
Sbjct: 313 GVTHFDDGVIYVGNDEVKRMNPRKALADQLGYCSEDRKVSGIVGDLSIRENIMLSLQAKK 372

Query: 359 HYLRVGMFLDRKKEAETADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKV 418
              R+ +    KK+ E A ++I LL IKTPS  +KI  LSGGNQQK +L+RWLA  D K+
Sbjct: 373 GLRRIPL----KKQQEVAQKYIDLLDIKTPSMEKKIGDLSGGNQQKVLLARWLA-TDPKL 427

Query: 419 VILDEPTRGIDVGAKHEIYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGE 478
           +ILDEPTRGID+  K EI N+I +L+ +G AI+ ISSE  E++   DRI+V+R     GE
Sbjct: 428 LILDEPTRGIDINTKREIENLIVKLSRQGMAIIFISSEYEEMVRTCDRIIVLRDRHAVGE 487

Query: 479 LTRKDATEQSVLSL 492
           LT    ++ +++ +
Sbjct: 488 LTDNQISQDNIMKV 501



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 65/241 (26%), Positives = 113/241 (46%), Gaps = 8/241 (3%)

Query: 256 VRFAAKGIEGHALAQPASFEVRRGEIVGFFGLVGAGRSELMHLVYGADHKKGGELLLDGK 315
           +R  AK   G         ++R GE+    G  GAG+S L+ ++ G   +  G + L G+
Sbjct: 16  MRHIAKYFPGVKALDDVQLDLRAGEVHALMGENGAGKSTLIKVMTGVYERTSGTVTLHGQ 75

Query: 316 PIKVRSAGEAIRHGIVLCPEDRKEEGIVAMATVSENINISCRRHYLRVGMFLDRKKEAET 375
            I  ++  EA   GI    +   E  +    +V+EN+ I   R  +R G  +D  +    
Sbjct: 76  DINPKTPQEAQDLGISTVYQ---EVNLCPNLSVAENVYIG--RQPMRFGQ-IDWHRMNAD 129

Query: 376 ADRFIKLLKIKTPSRRQKIRFLSGGNQQKAILSRWLAEPDLKVVILDEPTRGIDVGAKHE 435
           A + ++ L I     +    + S   QQ   ++R   +    V+ILDEPT  +D     +
Sbjct: 130 AVKLLESLDIHVDVTKTLDSY-SVSVQQMIAIAR-AVDMSAGVLILDEPTSSLDSNEVAQ 187

Query: 436 IYNVIYQLAERGCAIVMISSELPEVLGVSDRIVVMRQGRISGELTRKDATEQSVLSLALP 495
           ++ +I  L ++  AI+ ++  + +V  +SDRI V+R GR  GE   KD  E  +++  + 
Sbjct: 188 LFAIIRHLRDQNMAILFVTHFMDQVYAISDRITVLRNGRYIGEYLAKDLPELDLVTKMIG 247

Query: 496 Q 496
           Q
Sbjct: 248 Q 248


Lambda     K      H
   0.320    0.136    0.385 

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: 593
Number of extensions: 31
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 508
Length adjustment: 34
Effective length of query: 478
Effective length of database: 474
Effective search space:   226572
Effective search space used:   226572
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:

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:

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:

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:

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