GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Paraburkholderia bryophila 376MFSha3.1

Align Inositol transport system permease protein (characterized)
to candidate H281DRAFT_03379 H281DRAFT_03379 monosaccharide ABC transporter membrane protein, CUT2 family

Query= reanno::WCS417:GFF2333
         (340 letters)



>FitnessBrowser__Burk376:H281DRAFT_03379
          Length = 343

 Score =  227 bits (578), Expect = 4e-64
 Identities = 139/357 (38%), Positives = 200/357 (56%), Gaps = 36/357 (10%)

Query: 1   MNAITDNKPATVPTKSRRRLPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMI 60
           M  IT  +   +  ++R+R    +  F  L  + ++   F       +   +   L+ + 
Sbjct: 1   MLEITSGRTQALDKQARQRRRDLIQKFAALGSLVVLIVAFSLT---SAAFFSVGNLMTVA 57

Query: 61  LQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVW 120
           LQV+ I  L +  T VIIT GIDLS GSVLAL+ + AA L +              +PV 
Sbjct: 58  LQVTSIAYLGVAATCVIITGGIDLSVGSVLALAGVAAALLVKAG------------VPVP 105

Query: 121 IPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYT 180
           + +A G+ VG   G +NG  +   G+PPFIATLGMM+ ARGLA   T  +PVS L D++ 
Sbjct: 106 VAMAGGMLVGAACGWVNGICVTRMGLPPFIATLGMMLVARGLALQITGARPVSGLGDAFG 165

Query: 181 AIGHGAM---------------------PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNM 219
            +G+GA+                     PV+I +++ V   + L  T  G++ YA+G N 
Sbjct: 166 ELGNGALFKVSHIGADGFPDTVFPGIPYPVVIMVILFVAVSVLLSRTSLGRHIYAVGSNA 225

Query: 220 QAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGT 279
           +AAR SG+NV+   +  Y ++GLLAG  G V  +R  T Q   G+ YELDAIA+AVIGGT
Sbjct: 226 EAARLSGVNVQGVKLFTYVLSGLLAGATGCVLMSRLVTAQPNEGVMYELDAIASAVIGGT 285

Query: 280 SLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKR 336
           SL GGVG I+GT IGA ++GV+ +G    GV ++IQ II G++I+  V IDQ RN++
Sbjct: 286 SLMGGVGTISGTAIGAFVIGVLRNGLNMNGVSSFIQQIIIGVVILGTVWIDQLRNRK 342


Lambda     K      H
   0.325    0.140    0.394 

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: 259
Number of extensions: 10
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: 340
Length of database: 343
Length adjustment: 29
Effective length of query: 311
Effective length of database: 314
Effective search space:    97654
Effective search space used:    97654
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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