GapMind for catabolism of small carbon sources

 

Aligments for a candidate for permease in Klebsiella michiganensis M5al

Align Histidine permease HisP (characterized)
to candidate BWI76_RS19685 BWI76_RS19685 lysine transporter

Query= SwissProt::A2RI97
         (477 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS19685 BWI76_RS19685 lysine
           transporter
          Length = 489

 Score =  498 bits (1281), Expect = e-145
 Identities = 237/469 (50%), Positives = 334/469 (71%), Gaps = 4/469 (0%)

Query: 7   VKRNLKQRHITMIALGGTIGTGLFLTSGATISQAGPWGAVLAYCFIGIMVYFVMTSLGEM 66
           ++R LK RH+TMIA+GG+IGTGLF+ SGATISQAGP GA+L+Y  IG+MVYF+MTSLGE+
Sbjct: 13  LRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYILIGLMVYFLMTSLGEL 72

Query: 67  ATYLPTSGSFSDYGGRYVDPAFGFALGWNYWLNGAITIAVDLTTAGLITQFWFPHLPSWI 126
           A ++P SGSF+ YG  YV+  FGFALGWNYW N A+TIAVDL  A L+  +WFP  P W+
Sbjct: 73  AAFMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVAAQLVMTYWFPDAPGWV 132

Query: 127 FSGIATVLIFIINVMAVGAFGETEYWLSTIKVITIVLFLAIGLLTIFGVLGQGNVDVVAN 186
           +S +   ++F++N ++V  FGE EYW S IKV T+++F+ +G++ IFG+         +N
Sbjct: 133 WSALFLGIMFLLNWISVKGFGEAEYWFSLIKVATVIIFIIVGVMMIFGIFKGAQPAGWSN 192

Query: 187 LTAGNHGFVGGISGFVGVLLIAGFSFQGTEMLGITAGESEDPGKTIPKAMNSIFWRILLF 246
               +  F GG +  +GV +I GFSFQGTE++GI AGESE+P K IP+A+  +FWRILLF
Sbjct: 193 WVIDDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESENPEKNIPRAVRQVFWRILLF 252

Query: 247 YIFSIIVIAAIINFKDPRLL-NPSSTAVMSPFTIVFKNIGFAVAASVMNAVILTSVISSA 305
           Y+F+I++I+ II + DP LL N      +SPFT+VF++ G   AA++MNAVILT+V+S+ 
Sbjct: 253 YVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSAAAIMNAVILTAVLSAG 312

Query: 306 NSVMYASTRILYSLGQEKGAPKFFGRTAKNGIPFYALLATTIICFIAFLTGIFGTQ-IYL 364
           NS MYASTR+LY+L  +  AP+ F + +K G+P  AL ATT+I  + FL+ +FG Q +YL
Sbjct: 313 NSGMYASTRMLYTLACDGKAPRIFSKLSKGGVPRNALYATTVIAGLCFLSSMFGNQTVYL 372

Query: 365 FLIDLSSLTGFLAWLGISVSHIRFRRAYIAQGKKLEDLPYKAKWFPFGPIVALLMTGAIA 424
           +L++ S +TGF+AWLGI++SH RFRR Y+ QG  L DLPY++ +FP GPI A ++   I 
Sbjct: 373 WLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGNDLNDLPYRSGFFPLGPIFAFVLCLIIT 432

Query: 425 I--NLDPAMLFSEHWGEGLALYAAIPIFIVLYFGYKWKYNTKIIPLEEV 471
           +  N +  +  +  WG   A Y  IP+F+V++FGYK    T+ +   E+
Sbjct: 433 LGQNYEAFLKDTIDWGGVAATYIGIPLFLVIWFGYKLAKGTRFVRYSEM 481


Lambda     K      H
   0.327    0.142    0.438 

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: 757
Number of extensions: 39
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: 477
Length of database: 489
Length adjustment: 34
Effective length of query: 443
Effective length of database: 455
Effective search space:   201565
Effective search space used:   201565
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 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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