GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aroP in Lactobacillus silagei IWT126

Align Arbuscular mycorrhizal fungal proline:H+ symporter, AAP1 (binds and probably transports nonpolar, hydrophobic amino acids) (characterized)
to candidate WP_054653911.1 CES79_RS01340 amino acid permease

Query= TCDB::Q2VQZ4
         (536 letters)



>NCBI__GCF_002217945.1:WP_054653911.1
          Length = 491

 Score =  309 bits (792), Expect = 1e-88
 Identities = 171/470 (36%), Positives = 259/470 (55%), Gaps = 23/470 (4%)

Query: 30  NGG--LKQDLKNRHMQMIAIGGAIGAGLFVGSGGALQKGGPAALLIGYLIIGIMLLCTCL 87
           NGG  +K+ LK RH+ MIA+GG+IG GLFV SG A+   GP   L+ Y+ +GIM+     
Sbjct: 8   NGGNEVKRSLKTRHLSMIALGGSIGTGLFVASGSAISTAGPGGGLLAYVALGIMVYFLMT 67

Query: 88  ALAEMAVLYPVNGAFFTYIVRFVDPSWGFAMGWQYALAWLTVLPFELIAASITIRFWRED 147
           +L EMA   PV+G+F TY  ++VDP+ GFAMGW Y   W   L  ++  A++ ++FW  +
Sbjct: 68  SLGEMATNMPVSGSFATYSTKYVDPALGFAMGWNYWFNWAITLAVDISTAALVMKFWLPN 127

Query: 148 INMAVWVSVFLVVLMGIQIFGVRGYGEVEFVLSIIKICACVGFIILGIVINCGGVGDQ-- 205
           +   +W ++ LV++  I    V+ +GE E+ +++IK+   V F+I+G     G +G    
Sbjct: 128 VPGWIWSTIILVMIFMINALTVKAFGETEYWMAMIKVVTVVIFLIVGFATIFGIMGGHAT 187

Query: 206 GYIGVKYWRDPGAFTSFKGFCAVFVVAAFSFGGTEMVGLAAAESANPRKSIPMASKQVFW 265
           G     Y + P          +VFVVA FSF GTE+VG+ A ESA P KS+P A  QVFW
Sbjct: 188 GLSNFTYKKAP-FVGGVPAILSVFVVAGFSFQGTELVGITAGESATPEKSVPKAINQVFW 246

Query: 266 RIAIFYILNLFIVGLILPANDPRLMGASGANTKASPFVLAIQDAGIKVLPSIMNAVITVA 325
           RI +FYIL +F++  ++P   P+L+G+S ++   SPF L  + AG+    S+MNAVI  +
Sbjct: 247 RILLFYILAIFVIACLIPYTSPKLLGSSASDIAISPFTLVFERAGLAAAASVMNAVILTS 306

Query: 326 VLSVANSCTFGSTRTIQAMAERNMAPNFFKYIDSKGRPLYCVILQIAFGLLAYIGAAPQG 385
           V+S ANS  + S+R + ++A  + AP +F++    G PL   +     G +A+I  +  G
Sbjct: 307 VISAANSGMYASSRMLYSLALDDFAPKYFEHTTKNGVPLRAQVATTIVGAIAFI-TSIAG 365

Query: 386 MEIFGWLLALTGLGFLFVWGSICLAHIRMRAGMKAQGINLGLIPYKTPFGVAGSYLGLGL 445
            E++ WL+A +GL     W  I ++H R R     QG  L  + Y   +   G  L   L
Sbjct: 366 PEVYSWLIAASGLTGFIAWVGIAISHFRFRRAFVKQGHQLSELKYHAKWFPFGPILAFVL 425

Query: 446 NILALIASFYTALFPASGASPTAEAFFS------SYLAFFSVTLLYLGYK 489
            IL +I           G +P+A   F       +YL+     +L+  YK
Sbjct: 426 CILVII-----------GQNPSAFVHFDWKQIGVTYLSVPLFFILFFWYK 464


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: 630
Number of extensions: 33
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: 536
Length of database: 491
Length adjustment: 35
Effective length of query: 501
Effective length of database: 456
Effective search space:   228456
Effective search space used:   228456
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