GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04257 in Paraburkholderia bryophila 376MFSha3.1

Align ABC transporter for D-Cellobiose and D-Salicin, permease component 1 (characterized)
to candidate H281DRAFT_00168 H281DRAFT_00168 carbohydrate ABC transporter membrane protein 2, CUT1 family

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



>FitnessBrowser__Burk376:H281DRAFT_00168
          Length = 285

 Score =  327 bits (839), Expect = 2e-94
 Identities = 151/286 (52%), Positives = 209/286 (73%), Gaps = 2/286 (0%)

Query: 20  KPRRTLSRRNIIVYGTLIVVALYYLLPLYVMIVTSLKGMPEIRVGNIFAPPLEITFEPWV 79
           +P+ T+SR   ++Y  L++ ALY+L PLYVM+ TS K + ++R GN+  PP   T EPW+
Sbjct: 2   QPKMTISRA--VIYAALVLFALYFLFPLYVMLSTSFKDIDQLRTGNLLTPPSHWTVEPWI 59

Query: 80  KAWAEACTGLNCDGLSRGFWNSVRITVPSVIISIAIASVNGYALANWRFKGADLFFTILI 139
           KAW+ ACTG+ CDG+   F NSVR+ +P+V++S  I + NGY L +WRF+GAD  FT+L+
Sbjct: 60  KAWSGACTGVRCDGMQPFFMNSVRMVIPAVLLSSIIGAFNGYVLTHWRFRGADPIFTMLL 119

Query: 140 VGAFIPYQVMIYPIVIVLREMGVYGTLTGLIIVHTIFGMPILTLLFRNYFAGLPEELFKA 199
           VG FIP+Q ++ P+      +G+  T TGL++VH I+G+   T+ FRN++  +P EL KA
Sbjct: 120 VGCFIPFQAILLPMARFEGFLGLSNTTTGLVVVHVIYGIAFTTMFFRNFYVSIPAELVKA 179

Query: 200 ARVDGAGFWTIYFKIMLPMSLPIFVVAMILQVTGIWNDFLFGVVFTRPEYYPMTVQLNNI 259
           AR+DGAGF+TI+ KI+LP+SLPIF+V +I Q T IWNDFLFG+VF+  +  P+TV LNN+
Sbjct: 180 ARIDGAGFFTIFTKILLPVSLPIFMVCLIWQFTQIWNDFLFGIVFSGVDSMPITVALNNL 239

Query: 260 VNSVQGVKEYNVNMAATILTGLVPLTVYFVSGRLFVRGIAAGAVKG 305
           VN+  GVKEYNV+MA  I+  L  L VY V+GR FVRG+ AGAVKG
Sbjct: 240 VNTSTGVKEYNVDMAGAIIAALPTLLVYIVAGRYFVRGLTAGAVKG 285


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: 299
Number of extensions: 9
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: 305
Length of database: 285
Length adjustment: 26
Effective length of query: 279
Effective length of database: 259
Effective search space:    72261
Effective search space used:    72261
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