GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malK in Pseudomonas simiae WCS417

Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate GFF5028 PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein

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



>FitnessBrowser__WCS417:GFF5028
          Length = 370

 Score =  250 bits (638), Expect = 5e-71
 Identities = 133/285 (46%), Positives = 189/285 (66%), Gaps = 6/285 (2%)

Query: 4   VTLRDICKSYDGTP-ITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLI 62
           V+ R + KSYDG   I + ++L+I  GEF+  +GPSG GK+T L ++AG E  T+G++ +
Sbjct: 11  VSFRGVQKSYDGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQL 70

Query: 63  DNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQ 122
             + +N++PP  R +GMVFQ+YAL+PHMTVAEN+AF L + ++ K +I  RV+ V  ++Q
Sbjct: 71  AGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLSVRALSKTDISERVKRVLSMVQ 130

Query: 123 LDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQR 182
           LD   +R P  LSGGQ+QRVA+ R +V EP++ L DEPL  LD  LR  M++EI  LHQR
Sbjct: 131 LDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQR 190

Query: 183 IRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFV 242
           +  T++YVTHDQ EA+T++D++ V + GEI Q+  P  LY  PKN FVA F+G  + N +
Sbjct: 191 LGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAAPRTLYEEPKNTFVANFIG--ENNRL 248

Query: 243 EVRAISASPETVTIELPSGYPL-TLPVDGSAVSPGDPLTLGIRPE 286
             R  S S E   +EL  G  +  L V+   V  G P+TL +RPE
Sbjct: 249 NGRLHSHSGERCVVELARGEKVEALAVNVGQV--GGPVTLSVRPE 291


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: 398
Number of extensions: 18
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: 371
Length of database: 370
Length adjustment: 30
Effective length of query: 341
Effective length of database: 340
Effective search space:   115940
Effective search space used:   115940
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: 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