GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS24010 in Pseudomonas fluorescens FW300-N1B4

Align Polar amino acid ABC transporter, inner membrane subunit (characterized, see rationale)
to candidate Pf1N1B4_4398 Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)

Query= uniprot:B2TBJ8
         (250 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4398
          Length = 232

 Score =  177 bits (450), Expect = 1e-49
 Identities = 90/220 (40%), Positives = 140/220 (63%)

Query: 1   MHFDFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYIL 60
           M  D++ +++ +         TL + F SL LG +L++ +  MRVS   L N  A  Y  
Sbjct: 1   MILDYNLIWENLPLYFNGALLTLKVLFISLALGLVLAIPLALMRVSRSPLINFPAWLYTY 60

Query: 61  VFRGSPLLIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGL 120
           V RG+P+L+Q+FL+YYG+ QF  +R+S LWP L     CA L+ A+ T+ Y+AE++ G L
Sbjct: 61  VIRGTPMLVQLFLIYYGLAQFEAVRQSVLWPYLSSATFCACLAFAINTSAYSAELLAGSL 120

Query: 121 MAVPVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEV 180
            + P G+IEA  ++G+S   L RR++ P ALR+ LP YS E ++++++T+LAS+VT+ ++
Sbjct: 121 KSTPHGEIEAAKAMGMSRLTLYRRILMPSALRRALPQYSNEVLMMLQTTSLASIVTLVDI 180

Query: 181 TGVAQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLE 220
           TG A+ +  + Y   E FI A LIYL L F++VRL  + E
Sbjct: 181 TGAARTVSSRFYLPFEAFITAGLIYLALTFILVRLFKLAE 220


Lambda     K      H
   0.331    0.143    0.431 

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: 146
Number of extensions: 3
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: 250
Length of database: 232
Length adjustment: 23
Effective length of query: 227
Effective length of database: 209
Effective search space:    47443
Effective search space used:    47443
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 46 (22.3 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