GapMind for catabolism of small carbon sources

 

Alignments for a candidate for serP in Lactobacillus oryzae SG293

Align Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized)
to candidate WP_034527992.1 LOSG293_RS05505 amino acid permease

Query= TCDB::F2HQ24
         (457 letters)



>NCBI__GCF_000740055.1:WP_034527992.1
          Length = 458

 Score =  404 bits (1038), Expect = e-117
 Identities = 204/446 (45%), Positives = 298/446 (66%), Gaps = 2/446 (0%)

Query: 2   NTNQNEENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMY 61
           NTN  E N+   RGL+ RH+QLIA+ GTIGTGLFLGAG+SIHL GPSIIF YLI G + +
Sbjct: 4   NTNNQENNQELSRGLQGRHVQLIALGGTIGTGLFLGAGQSIHLAGPSIIFAYLITGIVCF 63

Query: 62  ILLRAIGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINF 121
           +L+RA+GE+L  D + HSF+ F+S+YLG+  G+   W+Y +  + +AMAEL A G Y+ +
Sbjct: 64  LLMRALGELLLSDLDAHSFIAFISKYLGKTWGFVAGWTYWICWLTIAMAELTASGLYLRY 123

Query: 122 WLPDLPIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYH 181
           W P+LP W+T + +L++L L+N++  + FGETEFWF +IKIVAI+GLI   I ++  HY 
Sbjct: 124 WFPNLPEWVTGIAILLILLLINSVTVRAFGETEFWFAIIKIVAILGLIAIGIYMVAVHYK 183

Query: 182 TGTDTVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAI 241
           T      V N+ KG   F NG + F  SFQMV+F+FV +E +GMTA+ET NP   + KAI
Sbjct: 184 TPVGYAEVGNLFKG-GLFANGSNGFLLSFQMVLFSFVGIEMVGMTASETANPTKIIPKAI 242

Query: 242 NQIPIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAAS 301
           + IP RI++FY+G+LLA+M IY W++I  ++SPFV +F  IGI+ AA ++NFVVLT+A S
Sbjct: 243 DDIPFRIIIFYLGSLLALMCIYPWQNISPNQSPFVQVFSAIGIRSAATIINFVVLTAAVS 302

Query: 302 ALNSALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSLLILFTPFISMIPAI 361
           A NS+LF+  R L+SL+     K+    +K S+  VP NAL F++++I  + F+++    
Sbjct: 303 ACNSSLFTTGRMLFSLTYGGKSKLSGKLSKLSRTQVPGNALRFSAIIIAASLFLNLFMP- 361

Query: 362 SNSFVFITSVATNLFLVVYLMTLITYLKYRKSSDFDPKGFVLPAAHIFIPLAIAGFVLIF 421
            + F FI+S+AT  FL ++   ++ +LKYRK+       F LP A     L +A    + 
Sbjct: 362 GHVFTFISSIATTCFLFIWGSIILAHLKYRKTKAAKSAKFKLPFAPFTDYLVLAFLAGVG 421

Query: 422 ISLFCFKDTIVPAIGSVIWVLIFGLF 447
           + L    +T++  IGS++W++    F
Sbjct: 422 LILLMKLETMIALIGSIVWLIALWAF 447


Lambda     K      H
   0.330    0.144    0.431 

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: 607
Number of extensions: 27
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: 457
Length of database: 458
Length adjustment: 33
Effective length of query: 424
Effective length of database: 425
Effective search space:   180200
Effective search space used:   180200
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 (21.8 bits)
S2: 51 (24.3 bits)

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

Links

Downloads

Related tools

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