GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04257 in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate GFF1859 Psest_1898 ABC-type sugar transport system, permease component

Query= reanno::Smeli:SMc04257
         (305 letters)



>FitnessBrowser__psRCH2:GFF1859
          Length = 280

 Score =  285 bits (729), Expect = 9e-82
 Identities = 135/286 (47%), Positives = 198/286 (69%), Gaps = 11/286 (3%)

Query: 20  KPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPWV 79
           +PR TL R  + +Y TL++    YL+PL VM++TS K   +IR GN+ + P   +   W+
Sbjct: 6   QPRLTLGR--LTIYATLLLACAVYLVPLIVMLLTSFKTPEDIRTGNLLSWPEAFSAMGWL 63

Query: 80  KAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILI 139
            AW         D +   FWNSV+I +P+V+IS A+ ++NGY L+ WRF+G+ LFF +L+
Sbjct: 64  TAW---------DSIGGYFWNSVKIVIPAVLISTALGALNGYVLSMWRFRGSQLFFGLLL 114

Query: 140 VGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKA 199
            G F+P+QV++ P    L ++G+  T TGL++VH ++G+   TL FRN++  +P+ L +A
Sbjct: 115 FGCFLPFQVILLPASFTLGKLGLANTTTGLVLVHVVYGLAFTTLFFRNFYVSVPDALVRA 174

Query: 200 ARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNI 259
           AR+DGAGF+TI+ +I+LPMS+PI +V +I Q T IWNDFLFGVVF   +  P+TV LNN+
Sbjct: 175 ARLDGAGFFTIFGRILLPMSVPIIMVCLIWQFTQIWNDFLFGVVFASGDTQPVTVALNNL 234

Query: 260 VNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305
           VN+  G K+YNV+MAA ++ GL  L VY V+G+ F+RG+ AGAVKG
Sbjct: 235 VNTSTGAKQYNVDMAAAMIAGLPTLVVYVVAGKYFLRGLTAGAVKG 280


Lambda     K      H
   0.329    0.145    0.450 

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: 278
Number of extensions: 4
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: 305
Length of database: 280
Length adjustment: 26
Effective length of query: 279
Effective length of database: 254
Effective search space:    70866
Effective search space used:    70866
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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