GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Bap2 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)



>FitnessBrowser__Koxy:BWI76_RS19685
          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 (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