GapMind for catabolism of small carbon sources

 

Alignments for a candidate for betS in Pseudomonas litoralis 2SM5

Align Glycine betaine/proline betaine transporter BetS (characterized)
to candidate WP_090276036.1 BLU11_RS18920 BCCT family transporter

Query= SwissProt::G3XCN6
         (706 letters)



>NCBI__GCF_900105005.1:WP_090276036.1
          Length = 555

 Score =  421 bits (1082), Expect = e-122
 Identities = 225/493 (45%), Positives = 309/493 (62%), Gaps = 22/493 (4%)

Query: 53  VNLPVFVGSVAVIALFVGIGVIAPKRAESIFSGMQTAILSGFGWLYLLSVAVFLFSMLFL 112
           ++  VF+ S   I LFV + +    +AE++FS ++  +     W +L +  +F+   L L
Sbjct: 52  IHSKVFLISAGAILLFVLLTLALQGQAEAVFSSLRGWVTGKMDWFFLGAANIFVVLCLAL 111

Query: 113 AFSRYGELKLGPDDSEPEFRYLSWIAMLFAAGMGIGLMYFAVGEPMTHFASPPEA----- 167
             S  G++++G  ++ P++ Y  W +MLFAAGMGIGLM++ V EP+ HF +  +      
Sbjct: 112 IVSPLGKVRIGGKEATPDYTYFGWFSMLFAAGMGIGLMFYGVAEPLGHFTAAYDGVVVGA 171

Query: 168 -------EPLTIAA------QREAMSVTFFHWGVHAWAIYSVVGLSLAYFGYRYNLPLTV 214
                   PL  AA       R  M+ T FHWG+H WAIY++V LSLA F Y   LPL+V
Sbjct: 172 DGVRTDWAPLGGAAGNAEEAMRLGMAATIFHWGLHPWAIYAIVALSLAIFSYNKGLPLSV 231

Query: 215 RSGLYPLLKEGIHGPIGHVVDIFAICGTMFGLATSLGFGILQINSGLNYLLGIPQSIYVQ 274
           RS  YPLL E I G  GHVVDI A+   MFGL TSLG G  Q ++G+ +L  IP +    
Sbjct: 232 RSIFYPLLGERIWGWPGHVVDILAVFAIMFGLVTSLGIGAQQASAGMEHLFNIPTTSLTM 291

Query: 275 LLLVTVVTAIATISVVTGVEKGVRILSETNLFLAVLLMLFVLVVGPTGTLMRDFVQNIGL 334
           +LL+  +TA+A  SVV GVEKGV+ LS+ NL LA+LL++FV+VVGPT  + +    N+G 
Sbjct: 292 VLLILAITAVALWSVVAGVEKGVQQLSKINLMLALLLLVFVIVVGPTLAIFKGLFSNLGA 351

Query: 335 YLDSLVLRTFNIYAYEPRPWIDSWTLFYWAWWISWSPFVGMFIARISRGRTVREFVTAVL 394
           Y+ S +    N    E   ++  WT FYWAWWISWSPFVGMFIAR+SRGRTVREF+ +V+
Sbjct: 352 YV-SYLPALANPVGREDVNFVQGWTAFYWAWWISWSPFVGMFIARVSRGRTVREFLVSVM 410

Query: 395 FVPAMFTFLWMTVFGNTAIYVDTTIANGELARDVKADLSVALFQFFEYLPWPAVTSTLAV 454
            VP++ + LWMT FG  AI  +  IA G      +A L + LF     LP  A+TS + +
Sbjct: 411 LVPSLVSVLWMTSFGGGAI--NQVIAEG-FTGVQEAALELQLFTMLSQLPLSAITSFIGI 467

Query: 455 LLVSIFFVTSSDSGSLVIDTIASGGETATPALQRIFWCSLSGIVAAVLLSTGGLTALQSA 514
           +LV +FF+TSSDSGSLVIDT+ +GG+   P  QR+FW  + G++A  LL  GGL ALQ+ 
Sbjct: 468 VLVIMFFITSSDSGSLVIDTVTAGGKVNAPVGQRVFWAIIEGVLAIALLLGGGLVALQAM 527

Query: 515 TISTALPFSLVML 527
            +ST LPF+LV+L
Sbjct: 528 AVSTGLPFTLVLL 540


Lambda     K      H
   0.326    0.139    0.422 

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: 1050
Number of extensions: 77
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: 706
Length of database: 555
Length adjustment: 38
Effective length of query: 668
Effective length of database: 517
Effective search space:   345356
Effective search space used:   345356
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: 54 (25.4 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