GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Lactobacillus oryzae SG293

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_034528196.1 LOSG293_RS05960 amino acid permease

Query= TCDB::Q2VQZ4
         (536 letters)



>NCBI__GCF_000740055.1:WP_034528196.1
          Length = 498

 Score =  309 bits (792), Expect = 1e-88
 Identities = 176/472 (37%), Positives = 257/472 (54%), Gaps = 9/472 (1%)

Query: 20  TRDVETGEVKNGGLKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIG 79
           +  V+  E++N  +K+ LK RH+ MIA+GG IG GLFV SG A+   GP   L+ Y+ +G
Sbjct: 4   SEQVQDTELENHEVKRGLKTRHVSMIALGGCIGTGLFVASGSAISSAGPGGALVAYIAMG 63

Query: 80  IMLLCTCLALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASI 139
           +M+     +L EMA   P++G+F  Y  ++VDP+ GFAMGW Y   W   +  ++  A++
Sbjct: 64  MMVYFLMTSLGEMATNMPISGSFAAYSAKYVDPALGFAMGWNYWFNWAITVAVDISTAAL 123

Query: 140 TIRFWREDINMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINC 199
            I+FW   +   +W +V LV+L  I    VR YGE EF LS+IKI   V F+++G++   
Sbjct: 124 VIKFWLPGVPGWIWSAVALVILFVINALSVRTYGETEFWLSLIKIVTIVVFLVVGLLTIF 183

Query: 200 GGVGDQ--GYIGVKYWRDPGAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIP 257
           G +G    G     Y + P     F    +VFVVA FSF GTE+VG+ A ES +P KS+P
Sbjct: 184 GIMGGHATGLENFTYKKAP-FVGGFPAILSVFVVAGFSFQGTELVGITAGESEDPHKSVP 242

Query: 258 MASKQVFWRIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSI 317
            A  QVFWRI +FYIL + ++ LI+P     L+G+S  +   SPF L  Q AG+    SI
Sbjct: 243 KAINQVFWRIILFYILAIAVIALIIPYTSHDLLGSSATDVAISPFTLVFQRAGLAAAASI 302

Query: 318 MNAVITVAVLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLA 377
           MNAVI  +VLS ANS  + STR + ++A    AP  F      G P+  ++       + 
Sbjct: 303 MNAVILTSVLSSANSGMYASTRMLYSLAHEGYAPKAFGRTTKNGIPMLALVGTTLIAAVT 362

Query: 378 YIGAAPQGMEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVA 437
           +I +   G +++ WL+A +GL     W  I ++H R R     QG +L  + Y   +   
Sbjct: 363 FISSI-AGPQLYLWLVAASGLTGFIAWIGIAISHFRFRRAFIKQGHDLSELKYHAKWFPI 421

Query: 438 GSYLGLGLNILALIASFYTALFPASGASPTAEAFFSSYLAFFSVTLLYLGYK 489
           G  L L L I  +I        PAS A+        +Y++   V +LY+ YK
Sbjct: 422 GPILALILCIGVIIGQ-----DPASFANFNWTQILVTYISVPLVLVLYIVYK 468


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: 628
Number of extensions: 23
Number of successful extensions: 3
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: 498
Length adjustment: 35
Effective length of query: 501
Effective length of database: 463
Effective search space:   231963
Effective search space used:   231963
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