GapMind for catabolism of small carbon sources

 

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

Align uncharacterized amino-acid permease C869.11 (characterized)
to candidate Pf1N1B4_1639 transport permease protein of gamma-aminobutyrate

Query= CharProtDB::CH_091412
         (580 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1639
          Length = 464

 Score =  207 bits (528), Expect = 6e-58
 Identities = 131/400 (32%), Positives = 199/400 (49%), Gaps = 16/400 (4%)

Query: 73  LKRSLKSRHMQMISIGGAIGTGLYVGSGSSLADGGPASVIINYSLIGIMMFFIVYALGEM 132
           L++ LK RH+ M+SI G IG GL+VGSG ++A  GPA V++ Y+  G ++  ++  LGEM
Sbjct: 11  LEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPA-VLLAYAAAGALVVLVMRMLGEM 69

Query: 133 AVAYPVAGGFNTYATRFIDPAWGFAVSWNYFINYFVTFPLELTTCAITFRYWTDINSAAW 192
           AVA P  G F+TYA R I    GF + W Y+  + +  PLE    A     W   N A W
Sbjct: 70  AVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFP-NVAIW 128

Query: 193 ISIFLVVIIIV--NLFGVRAYGEVEFILSTVKVVATFGFIILAIIINCGGVPTDHRGYIG 250
               ++ +++   NLF V+ YGE EF  + VKV+A  GFI L I+   G +PT     + 
Sbjct: 129 AFTLVITLLLTATNLFSVKNYGEFEFWFALVKVIAIIGFIGLGILAIFGFLPTSQVSGVS 188

Query: 251 GSIIKHKPFRHGFKGFCSVFTTAAFSFSGTEVIGLAAAEVDNPQKALPHAVKQVFWRIAI 310
                     +G         T  FSF GTE++ +AAAE  NP + +  A   V WRI +
Sbjct: 189 HLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRIGL 248

Query: 311 FYVVSLILIGLLISPDDPNLMGNGSTSVSPFVLAIKEANIKGLPSVFNAVIIISVVSVTN 370
           FY+VS+ ++  L+  +DP L      SV  +   ++   I     + + V++++V S  N
Sbjct: 249 FYLVSIFIVVALVPWNDPIL-----ASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSCLN 303

Query: 371 SSTYTAGRTLHGMANLKQAPSFFKYTDRLGRPLLAMIVVLLFGFFAYINEADKNGNDVSD 430
           S+ YTA R +  +     AP+  + T+  G P  A+++     F A         N V+ 
Sbjct: 304 SALYTASRMMFSLGKRGDAPAVSQRTNSSGTPYWAVMLSTAAAFLAVF------ANYVAP 357

Query: 431 -TVFNWLLALSGLSNFFTWGSICLCHIIFRLAFKKQGHSL 469
             VF +LLA SG      +  I +  +  R     +G  +
Sbjct: 358 AAVFEFLLASSGAIALLVYLVIAISQLRMRKQRMARGEKI 397


Lambda     K      H
   0.325    0.141    0.429 

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: 558
Number of extensions: 23
Number of successful extensions: 5
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: 580
Length of database: 464
Length adjustment: 35
Effective length of query: 545
Effective length of database: 429
Effective search space:   233805
Effective search space used:   233805
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: 52 (24.6 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