GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SM_b21216 in Klebsiella michiganensis M5al

Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate BWI76_RS06690 BWI76_RS06690 ABC transporter ATP-binding protein

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



>FitnessBrowser__Koxy:BWI76_RS06690
          Length = 369

 Score =  296 bits (758), Expect = 6e-85
 Identities = 152/288 (52%), Positives = 204/288 (70%), Gaps = 3/288 (1%)

Query: 1   MSALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDI 60
           MS + +RN+ KR+G   TL  +++ +E GEF V +G SGCGKSTLL +IAGL E S G++
Sbjct: 1   MSNIRLRNVTKRFGSTVTLHQVNLDIEDGEFAVFVGPSGCGKSTLLRMIAGLEEVSEGEV 60

Query: 61  LIGERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARL 120
           LIG+  +  V P  R +AMVFQSYALYP+++VA N+G+GL++ +VP+ E  + V   A+ 
Sbjct: 61  LIGDEVMNDVVPAHRGVAMVFQSYALYPHMTVAENMGYGLKVNKVPKDEIRRQVEMVAKT 120

Query: 121 LQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLH 180
           LQ+ +LLDRKP QLSGGQRQRVAIGRA+VRNP+VF+FDEPLSNLDA+LR+EMR  + +LH
Sbjct: 121 LQLSHLLDRKPKQLSGGQRQRVAIGRAIVRNPRVFMFDEPLSNLDAELRVEMRLHIAKLH 180

Query: 181 QMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMN 240
             L+TT+VYVTHDQ+EAMTLA +I VM  G++EQ+ +P  +Y  P   +VAGF+GSP MN
Sbjct: 181 HELKTTMVYVTHDQVEAMTLADKIVVMNYGKVEQMGSPMSLYYNPVNKFVAGFIGSPKMN 240

Query: 241 ILDAEMTA---NGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEAL 285
            L A +TA     L ++  ++              G  V +GIRPE L
Sbjct: 241 FLPATVTAWQPGQLSVKMAQDHNLTLNITTSPLQPGAAVTLGIRPEHL 288


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: 366
Number of extensions: 13
Number of successful extensions: 1
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