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_084937109.1 HA51_RS22655 amino acid permease

Query= CharProtDB::CH_003129
         (489 letters)



>NCBI__GCF_002095475.1:WP_084937109.1
          Length = 488

 Score =  860 bits (2222), Expect = 0.0
 Identities = 416/484 (85%), Positives = 457/484 (94%)

Query: 1   MVSETKTTEAPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYMLIGL 60
           M +++KTT+ PGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSY LIGL
Sbjct: 1   MHNDSKTTQQPGLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYALIGL 60

Query: 61  MVYFLMTSLGELAAYMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLV 120
           MVYFLMTSLGELAA+MPVSGSFATYG  YVEEGFGFALGWNYWYNWAVTIAVDLVA+QLV
Sbjct: 61  MVYFLMTSLGELAAFMPVSGSFATYGSKYVEEGFGFALGWNYWYNWAVTIAVDLVASQLV 120

Query: 121 MSWWFPDTPGWIWSALFLGVIFLLNYISVRGFGEAEYWFSLIKVTTVIVFIIVGVLMIIG 180
           M++WFPDTPGWIWSALFL ++FLLNYISV+GFGEAEYWFSLIKV TV++FI+VGVLMI G
Sbjct: 121 MNYWFPDTPGWIWSALFLCLMFLLNYISVKGFGEAEYWFSLIKVVTVVIFIVVGVLMITG 180

Query: 181 IFKGAQPAGWSNWTIGEAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESEDPAKNIPR 240
           I +GA+ AGW NWT+G+APFAGGFAAMIGVAMIVGFSFQGTELIGIAAGES+DPAKNIPR
Sbjct: 181 IMRGAENAGWHNWTVGDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESQDPAKNIPR 240

Query: 241 AVRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAVM 300
           AVRQVFWRILLFY+FAILIISLI+PYTDP LL NDV DI++SPFTLVFQ+AGLLSAAAVM
Sbjct: 241 AVRQVFWRILLFYIFAILIISLILPYTDPKLLHNDVTDIAISPFTLVFQNAGLLSAAAVM 300

Query: 301 NAVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFAKLSRGGVPRNALYATTVIAGLCF 360
           NAVILTAVLSAGNSGMYASTRML+ LA +GKAPRIF KLS+GGVPRNAL ATTV+AGLCF
Sbjct: 301 NAVILTAVLSAGNSGMYASTRMLFNLAREGKAPRIFGKLSKGGVPRNALIATTVVAGLCF 360

Query: 361 LTSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGHDINDLPYRSGFFPLG 420
           L+S FGNQ VYLWLLNTSGMTGFIAWLGIAISHYRFRRGYV QG ++ DLPYRSGFFPLG
Sbjct: 361 LSSKFGNQEVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVAQGLNLADLPYRSGFFPLG 420

Query: 421 PIFAFILCLIITLGQNYEAFLKDTIDWGGVAATYIGIPLFLIIWFGYKLIKGTHFVRYSE 480
           PIFAF+LCLIITLGQNY+AFL+D IDW GVAATYIGIPLFL+IW GYKL++G+ +V+YSE
Sbjct: 421 PIFAFVLCLIITLGQNYQAFLQDRIDWYGVAATYIGIPLFLLIWLGYKLVRGSRWVKYSE 480

Query: 481 MKFP 484
           M+FP
Sbjct: 481 MEFP 484


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: 1013
Number of extensions: 36
Number of successful extensions: 1
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: 488
Length adjustment: 34
Effective length of query: 455
Effective length of database: 454
Effective search space:   206570
Effective search space used:   206570
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: 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