GapMind for catabolism of small carbon sources

 

Alignments for a candidate for serP in Pantoea rwandensis LMG 26275

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_084934657.1 HA51_RS11575 D-serine/D-alanine/glycine transporter

Query= TCDB::F2HQ24
         (457 letters)



>NCBI__GCF_002095475.1:WP_084934657.1
          Length = 463

 Score =  345 bits (886), Expect = 1e-99
 Identities = 190/453 (41%), Positives = 272/453 (60%), Gaps = 8/453 (1%)

Query: 7   EENKPSQRGLKNRHIQLIAIAGTIGTGLFLGAGKSIHLTGPSIIFVYLIIGALMYILLRA 66
           E+ +  +R L NRHIQLIAI G IGTGLF+G+GK+I L GPSIIFVY+IIG +++ ++RA
Sbjct: 13  EQPEKLRRNLHNRHIQLIAIGGAIGTGLFMGSGKTISLAGPSIIFVYMIIGFMLFFVMRA 72

Query: 67  IGEMLYQDPNQHSFLNFVSRYLGEKPGYFIQWSYLLVVVFVAMAELIAIGTYINFWLPDL 126
           +GE+L  +    SF +F +  LG   GYF  W+Y    V   +A+++AI  Y   W P  
Sbjct: 73  MGELLLSNLEYKSFSDFAADLLGPWAGYFTGWTYWFCWVVTGIADVVAISAYFQLWFPGF 132

Query: 127 PIWMTEVFVLVLLTLLNTLNPKFFGETEFWFGMIKIVAIIGLILTAIILIFSHYHT--GT 184
            IWM+ +  +     LN    K FGE EFWF +IKIVAI+ LI+T I+L+  HY +  GT
Sbjct: 133 SIWMSALLCIFAFLALNIATVKLFGEMEFWFAIIKIVAIVALIITGIVLVSMHYPSPNGT 192

Query: 185 DTVSVTNITKGFEFFPNGLSNFFESFQMVMFAFVSMEFIGMTAAETDNPRPTLKKAINQI 244
            T S++NI      FP GLS FF  FQ+ +FAFV +E +G  AAET +P   L +AIN I
Sbjct: 193 -TASLSNIWDHGGMFPKGLSGFFAGFQIAVFAFVGIELVGTAAAETKDPHKVLPRAINAI 251

Query: 245 PIRIVLFYVGALLAIMSIYQWRDIPADKSPFVTIFQLIGIKWAAALVNFVVLTSAASALN 304
           P+RI++FYV ALL IM++  W  +  ++SPFV +F LIG+  AA++VNFVVLTSAAS+ N
Sbjct: 252 PVRIIMFYVLALLVIMAVTPWNQVLPNRSPFVEMFVLIGLPAAASIVNFVVLTSAASSAN 311

Query: 305 SALFSITRNLYSLSKLNNDKILKPFTKFSKAGVPVNALLFTSL-LILFTPFISMIPAISN 363
           S +FS +R L+ L++L      K F + S   VP   L F+ L L++    I +IP +  
Sbjct: 312 SGIFSTSRMLFGLAELG--VAHKAFGRLSARAVPTTGLFFSCLCLLVGVALIYLIPDVMT 369

Query: 364 SFVFITSVATNLFLVVYLMTLITYLKYRKS--SDFDPKGFVLPAAHIFIPLAIAGFVLIF 421
            F  +T+V+  LF+ V+ + L +YL YRK          F +P       + +A F  + 
Sbjct: 370 VFTMVTTVSAILFMFVWTIILCSYLAYRKQHPQRHAASKFKMPLGKFMCWVCMAFFAFVL 429

Query: 422 ISLFCFKDTIVPAIGSVIWVLIFGLFTFFKKIK 454
           + L   +DT    + + +W +I  L    ++ K
Sbjct: 430 VLLTLQEDTRQALMVTPLWFVILTLGWLLRRRK 462


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: 599
Number of extensions: 28
Number of successful extensions: 3
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: 463
Length adjustment: 33
Effective length of query: 424
Effective length of database: 430
Effective search space:   182320
Effective search space used:   182320
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.

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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