GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for D-Trehalose, permease component 1 (characterized)
to candidate Pf1N1B4_5113 Maltose/maltodextrin ABC transporter, permease protein MalF

Query= reanno::Smeli:SM_b20326
         (328 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5113
          Length = 295

 Score =  379 bits (973), Expect = e-110
 Identities = 181/296 (61%), Positives = 233/296 (78%), Gaps = 5/296 (1%)

Query: 28  VRSAWLFLAPTFLVLALVAGWPLIRTIYFSFTNASLTNLSGAEFVGFANYLSWITLKSGR 87
           VR+AWLFL P  L LALVA WPL+RT +FS T+A+L +  G  F+GF NYL      +G 
Sbjct: 1   VRAAWLFLTPMLLCLALVAAWPLLRTFWFSLTDANLADTGGGTFIGFGNYL----FHNGS 56

Query: 88  TIYRGLLADPAWWNAVWNTLKFTVLSVSIETALGLIVALVLNAQFPGRGLVRAAILIPWA 147
           + + G+L DP WWNAV NTL FTV+SV +E  LGL+VAL+LN +F GR LVRA ILIPWA
Sbjct: 57  S-WSGILVDPQWWNAVRNTLYFTVVSVGLEVVLGLLVALLLNIKFTGRALVRALILIPWA 115

Query: 148 IPTIVSAKMWAWMLNDQFGILNDMLIGLGLIGEKIAWTASPDTAMIAELIVDVWKTTPFM 207
           IPTIVSAK+W+WMLNDQFGI+N +++ LGLI   +AWTA  D +M A +IVDVWKT PF+
Sbjct: 116 IPTIVSAKIWSWMLNDQFGIINHLMLSLGLIDAPLAWTADADLSMWAVIIVDVWKTVPFV 175

Query: 208 ALLILAGLQMVPGDIYEAAKIDGVHPVRVFWRVTLPLIRPALMVAVIFRMLDALRIFDLI 267
            LL+LA LQM+P D YEAA++DG+HP++VFWRVTLPL+ PAL+VA IFR+LD+LR+FD+I
Sbjct: 176 TLLMLAALQMLPSDCYEAARVDGIHPLKVFWRVTLPLLMPALLVAAIFRILDSLRVFDVI 235

Query: 268 YVLTPNNAQTKTMSVMARENLFDFDKFAYGAAASTMLFLIIATITILYMWLGRLNL 323
           YVLT N++ T +MSV AR++L +F    YG+AAST+LFL++A I +LY++LGR  L
Sbjct: 236 YVLTSNSSSTMSMSVYARQHLVEFQDVGYGSAASTLLFLVVAVIALLYLYLGRRQL 291


Lambda     K      H
   0.328    0.140    0.438 

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: 416
Number of extensions: 12
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: 328
Length of database: 295
Length adjustment: 27
Effective length of query: 301
Effective length of database: 268
Effective search space:    80668
Effective search space used:    80668
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 (21.7 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