GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutW in Paraburkholderia bryophila 376MFSha3.1

Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate H281DRAFT_02451 H281DRAFT_02451 glycine betaine/proline transport system permease protein

Query= TCDB::Q9KKE2
         (285 letters)



>FitnessBrowser__Burk376:H281DRAFT_02451
          Length = 300

 Score =  248 bits (634), Expect = 9e-71
 Identities = 131/264 (49%), Positives = 183/264 (69%), Gaps = 3/264 (1%)

Query: 14  VNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFMALAC-RSSRRWSL 72
           V+  +  L+ +    F +I  VI      IE  L+ +P W ++  F+ +   R   R++L
Sbjct: 11  VDHGVHYLLDHDAKTFDSIGKVIEGFAALIEQGLQAVPMWALMAFFVGIGLWRVGWRFAL 70

Query: 73  TLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKSRVVRNITLPVLD 132
              +  LL  +   G WD  + TL L L +T++S+++GVP+GI  AKSR V  I  PVLD
Sbjct: 71  FTLLAMLL--IYGTGFWDQMVITLGLTLSSTLISLLLGVPLGIWTAKSRTVEMIVRPVLD 128

Query: 133 VMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFG 192
           +MQTMP+FVYLIPA MLFGLG+VP IL+T+I+A+PP +RLT LGI+ V+ E+VEA  AFG
Sbjct: 129 LMQTMPAFVYLIPAAMLFGLGRVPGILSTVIFAMPPAVRLTSLGIKHVNREIVEAGQAFG 188

Query: 193 GSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGK 252
            +P Q+L+ V+ P A P+IM G+NQTIMMALSMV++ASM+GA GLG  VL  IQ LD+G 
Sbjct: 189 CTPWQLLYKVQFPNALPSIMTGVNQTIMMALSMVIIASMVGAGGLGNDVLASIQRLDIGL 248

Query: 253 GLEAGIGIVILAVVLDRITQGFGK 276
           G E+G+ +V+LA++LDRIT+ FG+
Sbjct: 249 GFESGLSVVMLAIILDRITESFGR 272


Lambda     K      H
   0.327    0.142    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: 290
Number of extensions: 15
Number of successful extensions: 1
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: 285
Length of database: 300
Length adjustment: 26
Effective length of query: 259
Effective length of database: 274
Effective search space:    70966
Effective search space used:    70966
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: 48 (23.1 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