GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Pseudomonas stutzeri RCH2

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit

Query= reanno::psRCH2:GFF857
         (371 letters)



>FitnessBrowser__psRCH2:GFF4209
          Length = 383

 Score =  225 bits (574), Expect = 1e-63
 Identities = 117/286 (40%), Positives = 176/286 (61%), Gaps = 3/286 (1%)

Query: 9   ICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLIDNQRVN 68
           + K +D T     + L I  GE    +G SG GKSTLLR++AG E  T G + +D Q + 
Sbjct: 28  VTKKFDETVAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIFLDGQDIT 87

Query: 69  DLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQLDKLLE 128
           D+PP +R + M+FQSYAL+PHMTV +N+AFGLK   + K EI+ RV+ +  ++Q+ +  +
Sbjct: 88  DMPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDGLPKAEIEERVKEMLGLVQMTQYAK 147

Query: 129 RKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRIRSTMI 188
           RKP  LSGGQRQRVA+ R++ + PK+ L DEP+  LD  LR QM++E+ ++ +R+  T +
Sbjct: 148 RKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVQIIERVGVTCV 207

Query: 189 YVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVEVRAIS 248
            VTHDQ EAMT+A++I +++ G IAQVG P+ +Y  P +R V  F+G+  +N  +   I 
Sbjct: 208 MVTHDQEEAMTMAERIAIMHLGWIAQVGSPMDIYETPASRLVCEFIGN--VNLFDGELIE 265

Query: 249 ASPETVTIELPS-GYPLTLPVDGSAVSPGDPLTLGIRPEHFVMPDE 293
              +   I  P    P+ +    S  +    +T  IRPE  ++  E
Sbjct: 266 DMGDHAVIASPGLENPIYVGHGISTRAEDKQITYAIRPEKLLIGTE 311


Lambda     K      H
   0.322    0.139    0.405 

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: 319
Number of extensions: 8
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: 371
Length of database: 383
Length adjustment: 30
Effective length of query: 341
Effective length of database: 353
Effective search space:   120373
Effective search space used:   120373
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 (21.9 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