GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aroP in Klebsiella michiganensis M5al

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate BWI76_RS19685 BWI76_RS19685 lysine transporter

Query= TCDB::Q2VQZ4
         (536 letters)



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

 Score =  294 bits (752), Expect = 6e-84
 Identities = 168/494 (34%), Positives = 256/494 (51%), Gaps = 20/494 (4%)

Query: 17  VSETRDVETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYL 76
           VS+T+  E       GL+++LK RH+ MIAIGG+IG GLFV SG  + + GP   L+ Y+
Sbjct: 2   VSDTKTTEAP-----GLRRELKARHLTMIAIGGSIGTGLFVASGATISQAGPGGALLSYI 56

Query: 77  IIGIMLLCTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIA 136
           +IG+M+     +L E+A   PV+G+F TY   +V+  +GFA+GW Y   W   +  +L+A
Sbjct: 57  LIGLMVYFLMTSLGELAAFMPVSGSFATYGQNYVEEGFGFALGWNYWYNWAVTIAVDLVA 116

Query: 137 ASITIRFWREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIV 196
           A + + +W  D    VW ++FL ++  +    V+G+GE E+  S+IK+   + FII+G++
Sbjct: 117 AQLVMTYWFPDAPGWVWSALFLGIMFLLNWISVKGFGEAEYWFSLIKVATVIIFIIVGVM 176

Query: 197 INCGGVGDQGYIGVKYWR-DPGAFTS-FKGFCAVFVVAAFSFGGTEMVGLAAAESANPRK 254
           +  G        G   W  D   F   F     V ++  FSF GTE++G+AA ES NP K
Sbjct: 177 MIFGIFKGAQPAGWSNWVIDDAPFAGGFAAMIGVAMIVGFSFQGTELIGIAAGESENPEK 236

Query: 255 SIPMASKQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVL 314
           +IP A +QVFWRI +FY+  + I+ LI+P  DP L+     +   SPF L  Q AG+   
Sbjct: 237 NIPRAVRQVFWRILLFYVFAILIISLIIPYTDPSLLRNDVKDISVSPFTLVFQHAGLLSA 296

Query: 315 PSIMNAVITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFG 374
            +IMNAVI  AVLS  NS  + STR +  +A    AP  F  +   G P   +       
Sbjct: 297 AAIMNAVILTAVLSAGNSGMYASTRMLYTLACDGKAPRIFSKLSKGGVPRNALYATTVIA 356

Query: 375 LLAYIGAAPQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPF 434
            L ++ +      ++ WLL  +G+     W  I ++H R R G   QG +L  +PY++ F
Sbjct: 357 GLCFLSSMFGNQTVYLWLLNTSGMTGFIAWLGIAISHYRFRRGYVLQGNDLNDLPYRSGF 416

Query: 435 GVAGSYLGLGLNILALIASFYTALFPAS----GASPTAEAFFSSYLAFFSVTLLYLGYKA 490
              G      L ++  +   Y A    +    G + T       Y+      +++ GYK 
Sbjct: 417 FPLGPIFAFVLCLIITLGQNYEAFLKDTIDWGGVAAT-------YIGIPLFLVIWFGYKL 469

Query: 491 CTRKRQMYVRPAEM 504
              K   +VR +EM
Sbjct: 470 A--KGTRFVRYSEM 481


Lambda     K      H
   0.327    0.142    0.442 

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: 661
Number of extensions: 28
Number of successful extensions: 2
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: 536
Length of database: 489
Length adjustment: 35
Effective length of query: 501
Effective length of database: 454
Effective search space:   227454
Effective search space used:   227454
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