GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artM in Phaeobacter inhibens BS107

Align AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate GFF3834 PGA1_262p02380 putative histidine transport system permease protein HisM

Query= TCDB::O50183
         (232 letters)



>FitnessBrowser__Phaeo:GFF3834
          Length = 258

 Score =  154 bits (388), Expect = 2e-42
 Identities = 83/225 (36%), Positives = 129/225 (57%), Gaps = 8/225 (3%)

Query: 6   SVIWDSLPLY----FDGLLVTLKLLSISLLIGLLLAVPLALMRVSKQPLVNFPAWLYTYV 61
           S+ WD +P Y     +GL  T+ +L ++ ++G  LAVPL L +      ++ PA ++  V
Sbjct: 29  SLRWDWIPTYAPLALEGLWTTIWILVVTSILGFALAVPLGLAQAVGPWYLSTPARIFCTV 88

Query: 62  IRGTPMLVQLFLIYYGLA----QFDAVRESALWPWLSNASFCACLAFAINTSAYTAEILA 117
           IRGTP+L+Q++L+YYGL     QF  +R S LWP+L  A   A LA  ++ + Y  E++ 
Sbjct: 89  IRGTPLLLQIWLLYYGLGSLFPQFPWIRSSELWPYLRQAWPYAVLALTLSYAGYEGEVMR 148

Query: 118 GSLKATPHGEIEAAKAMGMSRLKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTL 177
           G+      G++EAAKA GM RL M+RRI LP A+R  LP    E I+ L+ T L + +T+
Sbjct: 149 GAFSGVAKGQLEAAKAYGMPRLTMFRRIWLPQAVRNVLPTLGGETILQLKATPLVATITV 208

Query: 178 VDITGAARTVYSQYYLPFEAFITAGLFYLCLTFILVRLFKLAERR 222
           +DI   +  V S  ++ +E  +   L Y+ +  ++   FK  E R
Sbjct: 209 LDIYAVSSRVRSDTFIVYEPLLLLALVYMAIAGVITLAFKRFEDR 253


Lambda     K      H
   0.330    0.140    0.425 

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: 187
Number of extensions: 10
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: 232
Length of database: 258
Length adjustment: 24
Effective length of query: 208
Effective length of database: 234
Effective search space:    48672
Effective search space used:    48672
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 (21.9 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