GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Klebsiella michiganensis M5al

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate BWI76_RS03270 BWI76_RS03270 sugar ABC transporter ATP-binding protein CymD

Query= reanno::Smeli:SMc04256
         (361 letters)



>FitnessBrowser__Koxy:BWI76_RS03270
          Length = 376

 Score =  299 bits (765), Expect = 9e-86
 Identities = 174/374 (46%), Positives = 232/374 (62%), Gaps = 16/374 (4%)

Query: 1   MTSVSVRDLSLNF-GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQ 59
           M +VS+R +   +      +  ++L+I  GEF+V +G SGC KST L  IAGL D+S G+
Sbjct: 1   MATVSLRKIEKRYENGFKAVHGIDLEIHDGEFMVFVGPSGCAKSTTLRMIAGLEDISGGE 60

Query: 60  IFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASE 119
           I+I +R V    PKDRGI MVFQ+YALYP  TV  N++FGLK+ K P  EI++RV+ A+E
Sbjct: 61  IYIGNRKVNDLPPKDRGIAMVFQNYALYPHKTVFDNMAFGLKMQKRPKDEIKRRVEDAAE 120

Query: 120 ILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRL 179
            L+I  LL RKP E+SGGQRQRVA+GRA+VR  DVFLFDEPLSNLDAKLR  +R++I +L
Sbjct: 121 KLEITELLYRKPKEMSGGQRQRVAVGRAIVRKPDVFLFDEPLSNLDAKLRVSMRMKIAQL 180

Query: 180 HQSLKN-----TMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFI 234
           H+SLK      TMIYVTHDQ EALTL DRI V+  G I Q+  P  +YN P N FVA FI
Sbjct: 181 HRSLKEEGHPATMIYVTHDQTEALTLGDRICVLNHGNIMQVDTPTDLYNYPNNKFVASFI 240

Query: 235 GSPSMNFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTR--LQPG---QKVVLGLRPEHVK 289
           GSPS+N     +   + R +V    IA  V     H++  L  G   + V  G+RPEH+ 
Sbjct: 241 GSPSINLIDTAIRKNNERLYVE---IAPGVEILIPHSKQVLLEGYINKPVCFGIRPEHIS 297

Query: 290 VDEARDGEPTHQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYP--PGSTVRLSFDM 347
           +    D   T + V+ + E MG++  L+    G+ +  R+  Q   P   G T+R + + 
Sbjct: 298 LASDDDDLNTFEGVLTVVENMGSEKFLYFIVGGKELIARVDTQDINPFHIGKTLRFNLNT 357

Query: 348 GVASIFDAESENRL 361
               +FD  +EN L
Sbjct: 358 AFCHVFDFYNENNL 371


Lambda     K      H
   0.320    0.137    0.392 

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: 355
Number of extensions: 10
Number of successful extensions: 4
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: 361
Length of database: 376
Length adjustment: 30
Effective length of query: 331
Effective length of database: 346
Effective search space:   114526
Effective search space used:   114526
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