GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03045 in Pseudomonas fluorescens GW456-L13

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate PfGW456L13_385 Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3433
         (232 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_385
          Length = 236

 Score =  192 bits (487), Expect = 6e-54
 Identities = 98/216 (45%), Positives = 142/216 (65%), Gaps = 1/216 (0%)

Query: 15  YLGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRGTPMLVQLFLI 74
           ++ GL  TL LL+ S+FFG + ++PL + RVS    V      +TY+ RGTP+ +QL + 
Sbjct: 19  HITGLAMTLWLLSASIFFGFVMSIPLSIARVSTNVWVRWPVQFYTYLFRGTPLYIQLLIC 78

Query: 75  YYGLAQFEAVR-ESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAKA 133
           Y G+    AVR +  L  +   A  C  LAFA+NT AYT EI AG++R+  +GE+EAAKA
Sbjct: 79  YTGIYSLAAVRAQPVLDAFFRDAMNCTILAFALNTCAYTTEIFAGAIRSMAHGEVEAAKA 138

Query: 134 MGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQFYL 193
            G++  K+Y  +++PSALRR+LP YSNEVI+ML +T++A   T+ DI   AR  N+  +L
Sbjct: 139 YGLTGWKLYTYVIMPSALRRSLPYYSNEVILMLHSTTVAFTATIPDILKVARDANSATFL 198

Query: 194 PFEAYITAGVFYLCLTFILVRLFKMAEHRWLGYLAP 229
            F+++  A + YL +TF LV LF++AE RWL +L P
Sbjct: 199 TFQSFGIAALIYLAVTFSLVGLFRLAERRWLSFLGP 234


Lambda     K      H
   0.330    0.140    0.427 

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: 156
Number of extensions: 6
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: 236
Length adjustment: 23
Effective length of query: 209
Effective length of database: 213
Effective search space:    44517
Effective search space used:    44517
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