GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate H281DRAFT_04155 H281DRAFT_04155 sorbitol ABC transporter ATP-binding protein /mannitol ABC transporter ATP-binding protein

Query= reanno::Smeli:SM_b21216
         (360 letters)



>FitnessBrowser__Burk376:H281DRAFT_04155
          Length = 369

 Score =  299 bits (765), Expect = 9e-86
 Identities = 165/357 (46%), Positives = 225/357 (63%), Gaps = 7/357 (1%)

Query: 1   MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60
           M+++ +RNIRK Y + E ++ I++ +  GEF+V +G SGCGKSTL+ +IAGL + SGGD+
Sbjct: 1   MASVTLRNIRKAYDDTEVMRDINLDIADGEFVVFVGPSGCGKSTLMRMIAGLEDISGGDL 60

Query: 61  LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120
            I    +  V P  R IAMVFQSYALYP++++  N+ FGL++    + E D AVR+ A++
Sbjct: 61  TINGTRMNDVPPAKRGIAMVFQSYALYPHMTLYDNMAFGLKLAGTKKPEIDAAVRNAAKI 120

Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180
           L I++LLDRKP QLSGGQRQRVAIGRA+ R P+VFLFDEPLSNLDA LR++MR E  RLH
Sbjct: 121 LHIDHLLDRKPKQLSGGQRQRVAIGRAITRKPKVFLFDEPLSNLDAALRVKMRLEFARLH 180

Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240
             L+TT++YVTHDQ+EAMTLA +I V+  G +EQ+ +P  +Y  PA  +VAGF+GSP MN
Sbjct: 181 DELKTTMIYVTHDQVEAMTLADKIVVLSAGNLEQVGSPTMLYHAPANRFVAGFIGSPKMN 240

Query: 241 ILDA---EMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLT 297
            ++     +T +G+ +          A   GA   G +V VGIRPE L +  G     ++
Sbjct: 241 FMEGVVQSVTHDGVTVRYETGETQRVAVEPGAVKQGDKVTVGIRPEHLHV--GMTDDGVS 298

Query: 298 ASVEVVELTGPE--LVTTATVGSQRITACLPPRTAVGMGSAHAFTFDGTALHLFDPE 352
           A    VE  G    L   ++V    + A +PP      G            HLFD E
Sbjct: 299 ARTMAVESLGDAAYLYAESSVAPDGLIARIPPLERHAKGETQKLGATPEHCHLFDSE 355


Lambda     K      H
   0.320    0.136    0.385 

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: 363
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: 360
Length of database: 369
Length adjustment: 29
Effective length of query: 331
Effective length of database: 340
Effective search space:   112540
Effective search space used:   112540
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: 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