GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AGP1 in Lactobacillus oryzae SG293

Align general amino acid permease AGP1 (characterized)
to candidate WP_034528194.1 LOSG293_RS05955 amino acid permease

Query= CharProtDB::CH_091105
         (633 letters)



>NCBI__GCF_000740055.1:WP_034528194.1
          Length = 485

 Score =  283 bits (725), Expect = 9e-81
 Identities = 165/490 (33%), Positives = 262/490 (53%), Gaps = 26/490 (5%)

Query: 113 SDSLKKTIQPRHVLMIALGTGIGTGLLVGNGTALVHAGPAGLLIGYAIMGSILYCIIQAC 172
           S  +K+ ++ RHV MIALG  IGTGL V +G+A+  AGP G L+ Y  MG ++Y ++ + 
Sbjct: 7   SHQVKRELKTRHVSMIALGGSIGTGLFVASGSAISTAGPGGALVAYTAMGLMVYFLMTSL 66

Query: 173 GEMALVYSNLTGGYNAYPSFLVDDGFGFAVAWVYCLQWLCVCPLELVTASMTIKYWTTSV 232
           GEMA  Y  ++G + AY +  VD   GFA+ W Y   W     +++ TA++ +K+W   +
Sbjct: 67  GEMA-TYMPVSGSFAAYATKYVDPAMGFAMGWNYWFNWAITLAVDISTAALVMKFWLPDI 125

Query: 233 NPDVFVIIFYVLVITINIFGARGYAEAEFFFNCCKILMMTGFFILGIIIDVGGAGNDGFI 292
              ++ ++  V++  +N    + + E+E++    K++ +  F  +G+      A   G +
Sbjct: 126 PGWIWSVLVLVIIFMLNALTVKAFGESEYWMAMIKVVTVFIFLAVGV------ATIFGIM 179

Query: 293 GGKYWHDPGAFNGKHAIDRFKG----VAATLVTAAFAFGGSEFIAITTAEQSNPRKAIPG 348
           GG   H  G  N       F G    + +  V A F+F G+E + IT  E  +P K+IP 
Sbjct: 180 GG---HATGLENFTRKEAPFVGGIPTILSVFVVAGFSFQGTELVGITAGESKDPEKSIPK 236

Query: 349 AAKQMIYRILFLFLATIILLGFLVPYNSDQLLGSTGGGTKASPYVIAVASHGVRVVPHFI 408
           A  Q+ +RI+  ++ +I ++  ++PY S QLLGS+      SP+ +     G+      +
Sbjct: 237 AINQVFWRIILFYILSIFVIACIIPYTSPQLLGSSASDIAISPFTLVFQRAGLAAAASVM 296

Query: 409 NAVILLSVLSMANSSFYSSARLFLTLSEQGYAPKVFSYIDRAGRPLIAMGVSALFAVIAF 468
           NAVIL SV+S ANS  Y+S+R+  +L+ QGYA K F+   R G PL A  ++ +   + F
Sbjct: 297 NAVILTSVISAANSGMYASSRMLYSLAVQGYASKAFTKTTRTGVPLNAQIMTTVVGALTF 356

Query: 469 CA--ASPKEEQVFTWLLAISGLSQLFTWTAICLSHLRFRRAMKVQGRSLGELGFKSQTGV 526
            A  A PK   ++ WL+A SGL+    W  I LSH RFRRA   QG  + EL + ++   
Sbjct: 357 IASIAGPK---IYIWLVAASGLTGFIAWLGIALSHFRFRRAFIKQGHHISELKYHAKLFP 413

Query: 527 WGSAYACIMMILILIAQFWVAIAPIGEGKLDAQAFFENYLAMPILIALYVGYKVWHKDWK 586
            G  +A I+ +LI++ Q   A         + Q     YL++PI I LY  YK+ ++   
Sbjct: 414 IGPIFALILCLLIIVGQDLDAFT-----NFNWQQISITYLSVPIFIGLYSYYKIRYR--T 466

Query: 587 LFIRADKIDL 596
             I  +KIDL
Sbjct: 467 KLISLEKIDL 476


Lambda     K      H
   0.324    0.138    0.424 

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: 705
Number of extensions: 38
Number of successful extensions: 6
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: 633
Length of database: 485
Length adjustment: 36
Effective length of query: 597
Effective length of database: 449
Effective search space:   268053
Effective search space used:   268053
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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