GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Rhodobacter johrii JA192

Align Fructose import permease protein FruF (characterized)
to candidate WP_108223269.1 C8J29_RS11820 ABC transporter permease

Query= SwissProt::Q8G846
         (356 letters)



>NCBI__GCF_003046325.1:WP_108223269.1
          Length = 363

 Score =  136 bits (342), Expect = 1e-36
 Identities = 100/315 (31%), Positives = 162/315 (51%), Gaps = 19/315 (6%)

Query: 22  TWSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITMLQESARYLMIATGMTLVIST 81
           T S+V  I+LV+  +IF    L   + S     A  L  +LQ+ A   ++    TLV+ T
Sbjct: 42  TPSLVPLIVLVVSVSIFGA-LLGQKFFS-----AFTLTLILQQVAIVGIVGAAQTLVVLT 95

Query: 82  AGIDLSVGSVMAVAGAAAMQ-TLSNGMNVWLSILIALAVGLAIGCVNGALVSFLGLQPFI 140
           AGIDLSVG++M ++     Q T   G+   LS+L  LA G  IG VNG LV+ + L PFI
Sbjct: 96  AGIDLSVGAIMVLSSVIMGQFTFRYGIPAPLSVLCGLAAGAGIGFVNGTLVARMKLPPFI 155

Query: 141 TTLIMMLAGRGMAKVITSGENTDASAVAGNEP-LKWFANGFILGIPA----------NFV 189
            TL M         + ++ E   +  ++   P L++F N F LG               V
Sbjct: 156 VTLGMWQIVLAANFLYSANETIRSQDISAQAPILQFFGNTFRLGADEAGRGGAVFTYGAV 215

Query: 190 IAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKPKKILFLVYAISGFLAAIAGLF 249
           + +++V+++  + R+TA G  + AVG + +A+ + G++ + +L  VY +SG + A+AG  
Sbjct: 216 LLILLVLVIAYVLRQTAWGRHVYAVGDDPDAAELAGVQTRNVLVTVYTLSGLICALAGWV 275

Query: 250 ATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSLAGSAVGAVIIAMIRKTIITLG 309
               +  V     GQ   + +I AVVIGG SL GG+ S+ G   GA+I+ +    +  +G
Sbjct: 276 MIGRLGSVSPT-AGQFANIESITAVVIGGISLFGGRGSVLGMLFGALIVGVFSLGLKLMG 334

Query: 310 VNAEATPAFFAVVVI 324
            + + T     +++I
Sbjct: 335 TDPQWTYLLIGMLII 349


Lambda     K      H
   0.325    0.136    0.384 

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: 283
Number of extensions: 23
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: 356
Length of database: 363
Length adjustment: 29
Effective length of query: 327
Effective length of database: 334
Effective search space:   109218
Effective search space used:   109218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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