GapMind for catabolism of small carbon sources

 

Aligments for a candidate for artM in Pseudomonas fluorescens GW456-L13

Align AotP aka AotM aka PA0890, component of Arginine/ornithine (but not lysine) porter (characterized)
to candidate PfGW456L13_3701 Histidine ABC transporter, permease protein HisM (TC 3.A.1.3.1)

Query= TCDB::O50183
         (232 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3701 Histidine
           ABC transporter, permease protein HisM (TC 3.A.1.3.1)
          Length = 232

 Score =  398 bits (1022), Expect = e-116
 Identities = 195/231 (84%), Positives = 222/231 (96%)

Query: 1   MIFDFSVIWDSLPLYFDGLLVTLKLLSISLLIGLLLAVPLALMRVSKQPLVNFPAWLYTY 60
           MI D+++IW++LPLYF+G L+TLK+L ISL +GL+LA+PLALMRVS+ PL+NFPAWLYTY
Sbjct: 1   MILDYNLIWENLPLYFNGALLTLKVLLISLALGLVLAIPLALMRVSRSPLINFPAWLYTY 60

Query: 61  VIRGTPMLVQLFLIYYGLAQFDAVRESALWPWLSNASFCACLAFAINTSAYTAEILAGSL 120
           VIRGTPMLVQLFLIYYGLAQF+AVR+SALWP+LS+A+FCACLAFAINTSAY+AE+LAGSL
Sbjct: 61  VIRGTPMLVQLFLIYYGLAQFEAVRQSALWPYLSSATFCACLAFAINTSAYSAELLAGSL 120

Query: 121 KATPHGEIEAAKAMGMSRLKMYRRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLVDI 180
           K+TPHGEIEAA+AMGMSRL +YRRIL+PSALRRALPQYSNEV+MMLQTTSLASIVTLVDI
Sbjct: 121 KSTPHGEIEAARAMGMSRLTLYRRILMPSALRRALPQYSNEVLMMLQTTSLASIVTLVDI 180

Query: 181 TGAARTVYSQYYLPFEAFITAGLFYLCLTFILVRLFKLAERRWLAYLAPRK 231
           TGAARTV S++YLPFEAFITAGLFYL LTFILVRLFKLAER WLAYLAPRK
Sbjct: 181 TGAARTVSSRFYLPFEAFITAGLFYLALTFILVRLFKLAERHWLAYLAPRK 231


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: 237
Number of extensions: 1
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: 232
Length of database: 232
Length adjustment: 23
Effective length of query: 209
Effective length of database: 209
Effective search space:    43681
Effective search space used:    43681
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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