GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc7a1 in Lactobacillus oryzae SG293

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_034526641.1 LOSG293_RS02350 amino acid permease

Query= CharProtDB::CH_091324
         (622 letters)



>NCBI__GCF_000740055.1:WP_034526641.1
          Length = 470

 Score =  247 bits (631), Expect = 7e-70
 Identities = 140/412 (33%), Positives = 227/412 (55%), Gaps = 29/412 (7%)

Query: 24  EESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALASVLAGLC 83
           ++++L + +N  DLV LGVG+ +G G+++L G VA   +GPAIVISF++A +    A +C
Sbjct: 21  KDAQLEKTMNAKDLVMLGVGAVIGTGIFILPGTVAALYSGPAIVISFILATIVCTFAAMC 80

Query: 84  YGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFDELIGKP 143
           Y EF + +P  GSAY Y  +  GE+  ++ GW LIL Y++  +SV+  WSA F   I   
Sbjct: 81  YAEFSSALPIAGSAYSYGNIVFGEVIGWVLGWALILEYMLAVASVSTGWSAYFLSFIK-- 138

Query: 144 IGEFSRQHMALNAPGVLAQTP--DIFAVIIIIILTGLLTLGVKESAMVNKIFTCINVLVL 201
            G       AL  P   A     +IFA+II++++  +++ G K S MVN I   + + ++
Sbjct: 139 -GFGISVPKALTGPFDPAHGTYINIFAIIIVLLIGLIISRGAKTSIMVNNIIVVVKIAII 197

Query: 202 CFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGVLSGAATCFYAFVG 261
              +  G       NW                      FMPFG  G+++GA+  F+A++G
Sbjct: 198 FLFLAVGLFYVKPTNWV--------------------PFMPFGVKGIMTGASLVFFAYLG 237

Query: 262 FDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYFCLDIDSPLPGAFK 321
           FD ++ +  EVKN +K +P+GI+ +LLIC I Y  V+A LT M  Y  L++  P+  A  
Sbjct: 238 FDVVSASAAEVKNAKKNMPIGIIGTLLICTILYILVAAVLTGMTSYTKLNVSDPVSFALH 297

Query: 322 --HQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFLAKINNRTKTPV 379
             +Q W      ++IG+L  + T ++  +F   R+IY++  DGLL K L KI  +  TP 
Sbjct: 298 LVNQNWVAG--IISIGALAGMFTMMVSMIFSSSRLIYSIGRDGLLPKALGKIEMKHHTPR 355

Query: 380 IATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLRYQPEQPN 431
           ++ +    I A++  L  L  L  L++IGTL+A++ ++  ++ LR + +  N
Sbjct: 356 VSLIAVTIIIAILGGLVSLDRLTQLVNIGTLIAFTFISIGIIPLRRRKDIDN 407



 Score = 60.5 bits (145), Expect = 2e-13
 Identities = 37/106 (34%), Positives = 55/106 (51%), Gaps = 3/106 (2%)

Query: 498 ALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGII--WRQPESKTKLSFKVPF 555
           +LI    I+A+LG     +     V + T  +    +  GII   R+ +      FKVP 
Sbjct: 357 SLIAVTIIIAILGGLVSLDRLTQLVNIGT-LIAFTFISIGIIPLRRRKDIDNAGGFKVPL 415

Query: 556 VPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHS 601
            PVLP++S  + I+++ QL   TW+  ++W LIG  IYF YG  HS
Sbjct: 416 YPVLPIVSAALCIFMLAQLPLDTWIVSSIWFLIGLAIYFLYGAKHS 461


Lambda     K      H
   0.324    0.138    0.417 

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: 753
Number of extensions: 34
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 622
Length of database: 470
Length adjustment: 35
Effective length of query: 587
Effective length of database: 435
Effective search space:   255345
Effective search space used:   255345
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: 40 (21.6 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