GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlE in Sporolactobacillus vineae SL153

Align PTS system glucitol/sorbitol-specific EIIB component; EII-Gut; Enzyme II-Gut; Glucitol/sorbitol-specific phosphotransferase enzyme IIB component; EC 2.7.1.198 (characterized)
to candidate WP_010631559.1 RH97_RS06580 PTS sorbitol transporter subunit IIB

Query= SwissProt::O32333
         (336 letters)



>NCBI__GCF_000246965.1:WP_010631559.1
          Length = 338

 Score =  457 bits (1177), Expect = e-133
 Identities = 224/339 (66%), Positives = 276/339 (81%), Gaps = 7/339 (2%)

Query: 1   MEKYNAIKIVKGSGGFGGPLTVKPEEGKDTLLYITGGGAEPEIVEKIVNLTGCKAVNGFK 60
           M +Y + K+V+G GGFGGPL + P EGKD ++YI GGG  P IV+K+V LTG   VNGFK
Sbjct: 1   MTEYKSAKVVRGHGGFGGPLIITPREGKDKIVYIVGGGNRPAIVDKLVELTGGVPVNGFK 60

Query: 61  TSVPEEQIFLVIIDCGGTLRCGIYPQKRIPTINVMPVGKSGPLAKFITEDIYVSAVGLNQ 120
           TSVP+E+I  +IIDCGGTLRCGIYP+K IPTINVMP GKSGPLA++ITE IYVS V ++Q
Sbjct: 61  TSVPDEKIAAIIIDCGGTLRCGIYPKKGIPTINVMPTGKSGPLAQYITEKIYVSNVTVDQ 120

Query: 121 ISLADSSAEPIKSTKVPEEG----KREFKYSADKKVSQSLAENSKSSIVQKIGMGAGKVV 176
           IS A   A P  +    + G    +R+FKYS DK +S++ A + + S++ +IG+GAGKV+
Sbjct: 121 ISAA---AGPASNESEQDAGAGAQQRQFKYSTDKTISKTKAASDQQSVLTRIGLGAGKVI 177

Query: 177 NTLYQAGRDAVQSMITTILPFMAFVAMLIGIIQGSGFGNWFAKILVPLAGNGIGLMILGF 236
           +T YQAGRD++Q+M+TTILPFMAFVAMLIG+IQGSG G  FAKI+ PLAGN  GL+++GF
Sbjct: 178 DTFYQAGRDSIQTMLTTILPFMAFVAMLIGVIQGSGIGTLFAKIMTPLAGNIWGLLLIGF 237

Query: 237 ICSIPLLSALLGPGAVIAQIVGTLIGVEIGKGTIPPSLALPALFAINTQCACDFIPVGLG 296
           +CS+P LS LLGPG VIAQI+GTLIGV+I +G +PP LALPALFAINTQ ACDF+PVGLG
Sbjct: 238 VCSLPFLSPLLGPGGVIAQIIGTLIGVQIAQGNVPPQLALPALFAINTQNACDFVPVGLG 297

Query: 297 LAEAEPETVEVGVPSVLYSRFMIGVPRVAVAWVASIGLY 335
           LAEA+PETVEVGVPSVLYSRF+ GVPRVA+AW+ S GLY
Sbjct: 298 LAEAKPETVEVGVPSVLYSRFLTGVPRVALAWLCSFGLY 336


Lambda     K      H
   0.319    0.139    0.405 

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: 537
Number of extensions: 25
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: 336
Length of database: 338
Length adjustment: 28
Effective length of query: 308
Effective length of database: 310
Effective search space:    95480
Effective search space used:    95480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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