GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc7a1 in Methylocystis bryophila S285

Align high affinity cationic amino acid transporter 1 (characterized)
to candidate WP_102938052.1 B1812_RS04230 amino acid permease

Query= CharProtDB::CH_091324
         (622 letters)



>NCBI__GCF_002117405.1:WP_102938052.1
          Length = 481

 Score =  263 bits (671), Expect = 2e-74
 Identities = 147/416 (35%), Positives = 226/416 (54%), Gaps = 25/416 (6%)

Query: 18  VVDCSREESRLSRCLNTYDLVALGVGSTLGAGVYVLAGAVARENAGPAIVISFLIAALAS 77
           + +   EE+ L R L    L+A+G+G  +GAG++VL G  A + AGP + ISFL++ LA 
Sbjct: 19  IAENDAEENGLKRALGWASLMAMGIGGIIGAGIFVLTGQAAADYAGPGVTISFLLSGLAC 78

Query: 78  VLAGLCYGEFGARVPKTGSAYLYSYVTVGELWAFITGWNLILSYIIGTSSVARAWSATFD 137
               LCY E  A +P  GS Y Y+YVT+GE++A+I GWNL+L Y  G ++VA  W+  F+
Sbjct: 79  TFVALCYAELAALIPAAGSTYTYTYVTLGEIFAWIIGWNLVLEYAAGAATVAVGWAGYFN 138

Query: 138 EL---IGKPIGE------FSRQHMALNAPGVLAQTPDIFAVIIIIILTGLLTLGVKESAM 188
            +   +G  + E      F+  H      GV     ++ A  II++LT LL  G  ES+ 
Sbjct: 139 RVMQGLGIHLPEALTSAYFANAHSIGGTHGVF----NVPAAAIILLLTALLMRGTSESSF 194

Query: 189 VNKIFTCINVLVLCFIVVSGFVKGSIKNWQLTEKNFSCNNNDTNVKYGEGGFMPFGFSGV 248
            N I   I V+V+  ++  G       NW               +      F  FG+SGV
Sbjct: 195 FNNIIVVIKVMVVLVVIFVGAAHVDAANWTPL------------IPENTDHFGHFGWSGV 242

Query: 249 LSGAATCFYAFVGFDCIATTGEEVKNPQKAIPVGIVASLLICFIAYFGVSAALTLMMPYF 308
           + GA+  F+A++GFD ++T  +E   PQ+ +P+GI+ SL+IC I Y  V+A  T ++ Y 
Sbjct: 243 VRGASVVFFAYIGFDGVSTAAQEAHTPQRDVPIGILGSLVICTILYVAVAAVATGVVSYK 302

Query: 309 CLDIDSPLPGAFKHQGWEEAKYAVAIGSLCALSTSLLGSMFPMPRVIYAMAEDGLLFKFL 368
            L +  P+       G     + V +G++  L+T++L  +F   R+ YAMA+DGLL K  
Sbjct: 303 ELGVPDPMALVMDRTGVAWLSWVVKLGAIAGLTTAILLLLFGQTRIFYAMAQDGLLPKVF 362

Query: 369 AKINNRTKTPVIATVTSGAIAAVMAFLFELKDLVDLMSIGTLLAYSLVAACVLVLR 424
           A ++   +TP ++    G   A+ A LF +  L +++SIGTL A++LV   VL LR
Sbjct: 363 AAVHPVWRTPAVSQALVGVFVALAAGLFPINILDEMVSIGTLAAFALVCGAVLHLR 418



 Score = 58.9 bits (141), Expect = 5e-13
 Identities = 38/119 (31%), Positives = 59/119 (49%), Gaps = 17/119 (14%)

Query: 486 GLIVNISAGLLAALIITVCIVAVLGREALAEGTLWAVFVMTGSVLLCMLVTGIIWRQPES 545
           G+ V ++AGL    I+          E ++ GTL A  ++ G+VL          R+ + 
Sbjct: 380 GVFVALAAGLFPINILD---------EMVSIGTLAAFALVCGAVLHL--------RRSQP 422

Query: 546 KTKLSFKVPFVPVLPVLSIFVNIYLMMQLDQGTWVRFAVWMLIGFTIYFGYGIWHSEEA 604
                F+ P +P +P+L I   + LM+ L   TW+R  VW  IG  IYF YG+ H++ A
Sbjct: 423 DMHRPFRAPGIPAMPLLGIASCLALMVALPLETWLRLIVWTAIGMAIYFFYGVKHAKRA 481


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: 709
Number of extensions: 36
Number of successful extensions: 3
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: 481
Length adjustment: 36
Effective length of query: 586
Effective length of database: 445
Effective search space:   260770
Effective search space used:   260770
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 Apr 09 2024. 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