GapMind for catabolism of small carbon sources

 

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

Align ABC transporter (characterized, see rationale)
to candidate H281DRAFT_04155 H281DRAFT_04155 sorbitol ABC transporter ATP-binding protein /mannitol ABC transporter ATP-binding protein

Query= uniprot:A0A166QFW2
         (381 letters)



>FitnessBrowser__Burk376:H281DRAFT_04155
          Length = 369

 Score =  363 bits (932), Expect = e-105
 Identities = 191/361 (52%), Positives = 248/361 (68%), Gaps = 2/361 (0%)

Query: 1   MIKLKLDNVNKQLGGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDL 60
           M  + L N+ K      ++RD++L+IA GEFVVFVGPSGCGKSTL+R+IAGL+ I GGDL
Sbjct: 1   MASVTLRNIRKAYDDTEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60

Query: 61  LIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQI 120
            I+G R+ND+ P +RG+ MVFQSYALYPHM++YDN++FGLKLA T K  +   V   A+I
Sbjct: 61  TINGTRMNDVPPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120

Query: 121 LQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLH 180
           L +D LL RKPK+LSGGQRQRVA+GRA+ R+P + LFDEPLSNLDA+LRV+MR E ARLH
Sbjct: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180

Query: 181 DRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRMN 240
           D L +TMIYVTHDQVEAMTLADKIVVL+ G +EQVGSP  LY  PA+RFVAGF+GSP+MN
Sbjct: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240

Query: 241 FLSARLQTPGETSLVDTLVWGITS-LPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGVV 299
           F+   +Q+     +      G T  +  +   +  G  +++GIRPEH+ +   D      
Sbjct: 241 FMEGVVQSVTHDGVTVRYETGETQRVAVEPGAVKQGDKVTVGIRPEHLHVGMTDDGVSAR 300

Query: 300 VTAVEYLGSETYVHLETG-QDEPLICRCEVSAGWQAGDRVELLLDLDNLHLFDADGVALS 358
             AVE LG   Y++ E+    + LI R         G+  +L    ++ HLFD++G A  
Sbjct: 301 TMAVESLGDAAYLYAESSVAPDGLIARIPPLERHAKGETQKLGATPEHCHLFDSEGKAFQ 360

Query: 359 R 359
           R
Sbjct: 361 R 361


Lambda     K      H
   0.320    0.137    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: 369
Number of extensions: 12
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: 381
Length of database: 369
Length adjustment: 30
Effective length of query: 351
Effective length of database: 339
Effective search space:   118989
Effective search space used:   118989
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 (21.8 bits)
S2: 50 (23.9 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