GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate H281DRAFT_02629 H281DRAFT_02629 carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-)

Query= reanno::pseudo3_N2E3:AO353_25895
         (367 letters)



>FitnessBrowser__Burk376:H281DRAFT_02629
          Length = 381

 Score =  371 bits (952), Expect = e-107
 Identities = 195/372 (52%), Positives = 269/372 (72%), Gaps = 12/372 (3%)

Query: 1   MAHLKIKNLQKGFEGFS-IIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGT 59
           MA + ++ +QK F+G + +++ ++LE+ + EF VF+GPSGCGKSTLLR++AGLE+ T G 
Sbjct: 1   MAAISLRGIQKTFDGNAPVLRDLNLEIGEHEFCVFLGPSGCGKSTLLRIVAGLEDQTDGD 60

Query: 60  IELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAAR 119
           + + GR +  V  A+R +AMVFQ+YAL+PHM+V +NM+F L LA   KAE+++KV EAA 
Sbjct: 61  VSIGGRTMNSVPAAERGVAMVFQSYALFPHMTVYENMAFGLKLARTPKAEIDRKVREAAH 120

Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179
           +L+L  +L RKP++LSGGQRQRVAIGRAIVR P +FLFDEPLSNLDAALR Q R+E+ARL
Sbjct: 121 VLQLDALLARKPRELSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDAALRGQTRIEIARL 180

Query: 180 HKE-LQATMIYVTHDQVEAMTLADKVVVLNG-------GRIEQVGSPLELYHQPANLFVA 231
           H+   QA+++YVTHDQ+EAMTLADK+V+L+        G I Q+G+PLELYH+P + FVA
Sbjct: 181 HQRYAQASVVYVTHDQIEAMTLADKIVLLHAGAETQRLGSIAQIGAPLELYHRPRSKFVA 240

Query: 232 GFLGTPKMGFLKGKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLA 291
           GF+G+P+M F+ G V R+   + EV +  GT + + + G  L  G  VTLGIRPEH+   
Sbjct: 241 GFIGSPRMNFIDGVVERIADDSVEVSM-PGTALRVLVDGRRLKPGQRVTLGIRPEHVRFD 299

Query: 292 LPGDCTLQVTADVSERLGSDTFCHVLTASGEALTMRIRGDLASRYGEQLSLHLDAEHCHL 351
             G  TL V A ++E+LG  ++ H   A G  L  +  GDL  R GE+L+LHL A+ CHL
Sbjct: 300 -GGTQTLAVNALLTEQLGEHSYLHADHAGG-TLIAKAPGDLHVRNGERLALHLPADACHL 357

Query: 352 FDANGVAVARPL 363
           FD +G+A+ R +
Sbjct: 358 FDEDGIALHRTI 369


Lambda     K      H
   0.321    0.137    0.390 

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: 409
Number of extensions: 17
Number of successful extensions: 5
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: 367
Length of database: 381
Length adjustment: 30
Effective length of query: 337
Effective length of database: 351
Effective search space:   118287
Effective search space used:   118287
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