GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate H281DRAFT_03228 H281DRAFT_03228 carbohydrate ABC transporter ATP-binding protein, CUT1 family

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>FitnessBrowser__Burk376:H281DRAFT_03228
          Length = 383

 Score =  364 bits (935), Expect = e-105
 Identities = 191/372 (51%), Positives = 260/372 (69%), Gaps = 14/372 (3%)

Query: 1   MANLKIKNLQKGF-EGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGT 59
           MA++ ++ +QK + +G  +I+ +DLE+ + EF VF+GPSGCGKSTLLR+IAGLE+++ G 
Sbjct: 1   MASISLRGVQKAYGDGAPVIRDVDLEIGENEFCVFLGPSGCGKSTLLRMIAGLEDLTDGD 60

Query: 60  IELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAAR 119
           + + G+ + +V  A+R +AMVFQ+YAL+PHM+V +NM+F L LA   K E+++KV EAAR
Sbjct: 61  LFIGGKVMNDVPAAQRGVAMVFQSYALFPHMTVFENMAFGLKLAKTPKDEIDRKVREAAR 120

Query: 120 ILELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRL 179
           IL+L  +LER+PK LSGGQRQRVAIGRAIVR P +FLFDEPLSNLDA LR Q R+E+ RL
Sbjct: 121 ILQLEALLERRPKALSGGQRQRVAIGRAIVRQPGVFLFDEPLSNLDATLRGQTRIEIARL 180

Query: 180 HKEL-QATMIYVTHDQVEAMTMADKVVVLNGGK-------IEQVGSPLDLYHQPANLFVA 231
           HK+  +A+++YVTHDQ+EAMT+ADK+V+L+ GK       I Q+G+PL+LYH+P + FVA
Sbjct: 181 HKQFAKASVVYVTHDQIEAMTLADKIVLLHAGKDTERYGSIAQIGAPLELYHRPRSRFVA 240

Query: 232 GFLGTPKMGFLKGKITRVDSQGCEVQLD-AGTRVSLPLGGRHLSVGSAVTLGIRPEHLEL 290
           GF+G+P+M FL G+I  VD+QG  V LD     V +P  G  L V  AVTLG+RPEHLE 
Sbjct: 241 GFIGSPRMNFLPGRIASVDAQGVVVTLDHTHENVRVPADGAALQVSQAVTLGVRPEHLEF 300

Query: 291 A----KPGDCALQVTADVSERLGSDTFCHVRTASGEALTMRVRGDLASRYGETLSLHLDA 346
           A       D  L  T  + E+LG  ++ H+    G AL  +  GD     G+  +L +  
Sbjct: 301 ADLSSSHDDAVLSRTVSLVEQLGEHSYVHLDQPGGVALIAKAPGDTRLAPGDRANLRVPR 360

Query: 347 QHCHLFDADGVA 358
              HLF  DG A
Sbjct: 361 HATHLFTEDGFA 372


Lambda     K      H
   0.320    0.137    0.389 

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: 430
Number of extensions: 15
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: 383
Length adjustment: 30
Effective length of query: 337
Effective length of database: 353
Effective search space:   118961
Effective search space used:   118961
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