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_084935844.1 HA51_RS17310 proline-specific permease ProY

Query= CharProtDB::CH_003129
         (489 letters)



>NCBI__GCF_002095475.1:WP_084935844.1
          Length = 451

 Score =  261 bits (668), Expect = 3e-74
 Identities = 150/395 (37%), Positives = 221/395 (55%), Gaps = 18/395 (4%)

Query: 9   EAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGLMVYFLMTS 68
           E   L+R L  RH+  +A+G +IGTGLF  S   I  AGP   LL+Y++ G + Y +M +
Sbjct: 3   ETNKLKRGLSTRHIRFMALGSAIGTGLFYGSADAIKMAGPS-VLLAYIIGGAIAYIIMRA 61

Query: 69  LGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMSWWFPDT 128
           LGE++   P + SF+ Y Q+Y+    G+  GW Y +   +    D+ A  + M  WFP+ 
Sbjct: 62  LGEMSVNNPQASSFSRYAQDYLGPLAGYITGWTYCFEILIVAIADVTAFGIYMGVWFPEV 121

Query: 129 PGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMII-GIFKGAQP 187
           P WIW    + +I  +N +SV+ FGE E+WFS  KV T+I+ I+ G  +I  GI  G QP
Sbjct: 122 PHWIWVLSVVLIIGGINLMSVKVFGEVEFWFSFFKVATIIIMILAGFGIIFWGIGNGGQP 181

Query: 188 AGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPRAVRQVFW 247
            G  N       FA G   M+    +V F++ G E+IGI AGE+EDPAK+IPRA+  V  
Sbjct: 182 TGIHNLWSNGGFFAHGIVGMLLSLQMVMFAYGGIEIIGITAGEAEDPAKSIPRAINSVPL 241

Query: 248 RILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVMNAVILTA 307
           RIL+FYV  + +I  I P+       N V     SPF L FQH G+ +AA+++N V++TA
Sbjct: 242 RILVFYVGTLFVIMSIYPW-------NQV-GTQGSPFVLTFQHLGIAAAASLLNFVVITA 293

Query: 308 VLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCFLTSMFGN 367
            LSA NS ++   RML+ +A  G AP++F   S  G P    + T V+  +  L +++ N
Sbjct: 294 SLSAINSDVFGVGRMLHGMAQQGHAPKVFTNTSDRGAP----WVTVVVMMVALLMAVYLN 349

Query: 368 ----QTVYLWLLNTSGMTGFIAWLGIAISHYRFRR 398
               + V+L + + +       W+ I +S   FRR
Sbjct: 350 YLMPEKVFLVIASLATFATVWVWIMILLSQIAFRR 384


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: 691
Number of extensions: 43
Number of successful extensions: 4
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: 451
Length adjustment: 33
Effective length of query: 456
Effective length of database: 418
Effective search space:   190608
Effective search space used:   190608
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