GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Pseudomonas stutzeri RCH2

Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit

Query= TCDB::Q00752
         (377 letters)



>FitnessBrowser__psRCH2:GFF4209
          Length = 383

 Score =  219 bits (558), Expect = 1e-61
 Identities = 131/340 (38%), Positives = 199/340 (58%), Gaps = 23/340 (6%)

Query: 2   VELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGE 61
           V L ++ + KK+  +   +V+D  L I   E    +G SG GKST LRM+AG E  T+G 
Sbjct: 21  VLLKIDRVTKKFDET--VAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGR 78

Query: 62  LKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQ 121
           + +DG+ + D  P +R I M+FQ+YAL+PHM+V  N+AFGLK     K  I++RVKE   
Sbjct: 79  IFLDGQDITDMPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDGLPKAEIEERVKEMLG 138

Query: 122 ILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKI 181
           ++ +T++ +RKP  LSGGQRQRVA+ R++ +  K+ L+DEP+  LD KLR  M+ E+ +I
Sbjct: 139 LVQMTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVQI 198

Query: 182 HRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKF 241
             R+G T + VTHDQ EAMT+A+RI IM           +G + QVG+P ++Y  PA++ 
Sbjct: 199 IERVGVTCVMVTHDQEEAMTMAERIAIMH----------LGWIAQVGSPMDIYETPASRL 248

Query: 242 VAGFIGSPAMNFFD----VTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRP 297
           V  FIG+  +N FD      + D  +++  GL   +  G      S   ++K + + IRP
Sbjct: 249 VCEFIGN--VNLFDGELIEDMGDHAVIASPGLENPIYVGH---GISTRAEDKQITYAIRP 303

Query: 298 EDISSSLLVQETYPDATVDAEVVVSEL--LGSETMLYLKL 335
           E +     + E        A+ VV ++  LG  ++ Y+KL
Sbjct: 304 EKLLIGTELPELERPGYNWAKGVVHDIAYLGGHSVYYIKL 343


Lambda     K      H
   0.318    0.135    0.375 

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: 332
Number of extensions: 13
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: 377
Length of database: 383
Length adjustment: 30
Effective length of query: 347
Effective length of database: 353
Effective search space:   122491
Effective search space used:   122491
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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