GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livJ in Sinorhizobium meliloti 1021

Align Solute-binding (Aliphatic amino acid) component of ABC transporter (characterized, see rationale)
to candidate SMc01946 SMc01946 leucine-specific binding protein

Query= uniprot:Q1MDE9
         (367 letters)



>FitnessBrowser__Smeli:SMc01946
          Length = 372

 Score =  336 bits (861), Expect = 7e-97
 Identities = 168/352 (47%), Positives = 230/352 (65%), Gaps = 1/352 (0%)

Query: 10  LVASLAFAPLAHADITIGLIAPLTGPVAAYGDQVKNGAQTAVDEINKKGGILGEKVVLEL 69
           L A +AF+  A ADI +G+  PLTGP AA+G Q++ GA+ A ++IN  GGI GE++ + L
Sbjct: 11  LTAMVAFSGTAWADILVGVGGPLTGPNAAFGAQLQKGAEQAAEDINAAGGINGEQIKVVL 70

Query: 70  ADDAGEPKQGVSAANKVVGDGIRFVVGPVTSGVAIPVSDVLAENGVLMVTPTATAPDLTK 129
            DD  +PKQGVS A K V DG++FVVG   SGV+IP S++ AENG+L VTP +T P  T+
Sbjct: 71  GDDVSDPKQGVSVAQKFVADGVKFVVGHFNSGVSIPASEIYAENGILQVTPASTNPQFTE 130

Query: 130 RGLTNVLRTCGRDDQQAEVAAKYVLKNFKDKRVAIVNDKGAYGKGLADAFKATLNAGGIT 189
           RGL N  RTCGRDDQQ  VA  Y+  NFKD +VA+++DK  YG+GLAD  K ++N  G+T
Sbjct: 131 RGLWNTFRTCGRDDQQGAVAGAYIAANFKDAKVAVIHDKTPYGQGLADETKKSMNEAGVT 190

Query: 190 EVVNDAITPGDKDFSALTTRIKSEKVDVVYFGGYHPEGGLLARQLHDLAANATIIGGDGL 249
           E + + I  GDKDFSAL  ++K   V +VY+GG H E GL+ RQ+ D    AT++ GDG+
Sbjct: 191 EALYEGINTGDKDFSALIAKMKQAGVSIVYYGGLHTEAGLIMRQMKDQGLKATMMSGDGI 250

Query: 250 SNTEFWAIGTDAAGGTIFTNASDATKSPDSKAAADALAAKNIPAEAFTLNAYAAVEVLKA 309
            + E  +I  DA  GT+ T A D  KSP +K   +   A     EA+TL AYAA++V+  
Sbjct: 251 VSNELASIAGDAVDGTLMTFAPDPRKSPAAKDLVEKFRAAGFEPEAYTLYAYAALQVIAE 310

Query: 310 GIEKAGSAEDAEAVATALKDGKEIPTAIGKVTYGETGDLTSQSFSLYKWEAG 361
           G + AG+  D +AVA A+K      TAIG++ + E GD+T   + +Y W+ G
Sbjct: 311 GAKAAGNT-DPQAVAEAIKAKGPFKTAIGELGFDEKGDITRPDYVMYTWKKG 361


Lambda     K      H
   0.312    0.131    0.362 

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: 446
Number of extensions: 23
Number of successful extensions: 2
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: 367
Length of database: 372
Length adjustment: 30
Effective length of query: 337
Effective length of database: 342
Effective search space:   115254
Effective search space used:   115254
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 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