GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Pantoea rwandensis LMG 26275

Align lysine-specific permease (characterized)
to candidate WP_084936496.1 HA51_RS20955 S-methylmethionine permease

Query= CharProtDB::CH_003129
         (489 letters)



>NCBI__GCF_002095475.1:WP_084936496.1
          Length = 469

 Score =  336 bits (862), Expect = 9e-97
 Identities = 182/466 (39%), Positives = 262/466 (56%), Gaps = 22/466 (4%)

Query: 6   KTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFL 65
           +T      +R +K RHL M+++GG IGTGLF  +G  IS  G  G LL+Y++  L+V+ +
Sbjct: 5   ETPSQDNFKRTMKVRHLVMLSLGGVIGTGLFFNTGYIISTTGAAGTLLAYLIGALVVWLV 64

Query: 66  MTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWF 125
           M  LGELA  MP +G+F  Y   Y+    G+ + W YW  W V +   L AA   M +WF
Sbjct: 65  MVCLGELAVAMPETGAFHVYAARYLSPATGYTVAWLYWLTWTVALGSSLTAAGFCMQYWF 124

Query: 126 PDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIGIF--- 182
           P TP W+W  +F   I+LLN +S R F E E+WFS+IKV T+I FII+G   + G     
Sbjct: 125 PTTPVWLWCLVFCIAIYLLNIVSTRFFAEGEFWFSIIKVVTIIAFIILGAGAMFGFIPMK 184

Query: 183 KGAQPAGWSNWTI-GEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRA 241
            G+   G SN T  G  P   G   ++   + V F+F GTELIGIAAGE+E P K +P A
Sbjct: 185 DGSAAPGLSNLTASGWLPH--GTLPILMTMVAVNFAFSGTELIGIAAGETEQPQKALPLA 242

Query: 242 VRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMN 301
           +R    R+++F++  + +++ +IP     +++        SPF LVF+  G+  AA + N
Sbjct: 243 IRTTVARLIIFFIGTVFVLAALIPMDQAGIVK--------SPFVLVFEKIGIPYAADIFN 294

Query: 302 AVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFL 361
            VILTA+LSA NSG+YAS RML++LA +   PR FA+++  GVP  AL  + +   L   
Sbjct: 295 FVILTAILSAANSGLYASGRMLWSLANENTLPRCFARVNHRGVPVLALTISMLGGLLALF 354

Query: 362 TSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLGP 421
           +S+    TV++ L   SG      WL I  SHY FRR ++  G  +  L YR+  +PL P
Sbjct: 355 SSVIAPDTVFVALSAISGFAVVAVWLSICASHYVFRRRHLQAGGTLQQLAYRAPLYPLTP 414

Query: 422 IFAFILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGY 467
           I  F+LCL+  +G  ++   +         A + GIP  L  +  Y
Sbjct: 415 ILGFLLCLLACVGLAFDPSQR--------IALWCGIPFVLFCYAAY 452


Lambda     K      H
   0.327    0.142    0.451 

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: 722
Number of extensions: 32
Number of successful extensions: 3
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: 489
Length of database: 469
Length adjustment: 34
Effective length of query: 455
Effective length of database: 435
Effective search space:   197925
Effective search space used:   197925
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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