GapMind for catabolism of small carbon sources

 

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

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate PfGW456L13_3150 L-proline glycine betaine ABC transport system permease protein ProV (TC 3.A.1.12.1)

Query= SwissProt::P17328
         (400 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3150 L-proline
           glycine betaine ABC transport system permease protein
           ProV (TC 3.A.1.12.1)
          Length = 372

 Score =  288 bits (736), Expect = 2e-82
 Identities = 160/355 (45%), Positives = 237/355 (66%), Gaps = 22/355 (6%)

Query: 3   IKLEVKNLYKIFGEHPQRAFK-YIEKGLSKEQILEKTGLSLGVKDASLAIEEGEIFVIMG 61
           + ++ ++++KIFG+    A    +++GL+K QIL+  G  +GV D SL +  GEIF IMG
Sbjct: 11  VLIDCQSVWKIFGKAAPAAMNAVVQQGLTKTQILQNYGCVVGVSDVSLQVRRGEIFCIMG 70

Query: 62  LSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREVRRKKIAMVFQSFALMPHM 121
           LSGSGKST++RLLN+LI P+ G++++ G +++ ++ A+LREVR + I MVFQS AL+P+ 
Sbjct: 71  LSGSGKSTLIRLLNKLITPSAGKIVVKGKELSSLNAAQLREVRARHIGMVFQSVALLPNR 130

Query: 122 TVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPDELSGGMRQRVGLARALAI 181
           TVL+NTAFG+E+ G+   ER + A  AL +VGL ++   YP ELSGGM+QRVGLARA+  
Sbjct: 131 TVLENTAFGLEVQGVGKAERYKVAEQALAKVGLSDWMSRYPSELSGGMQQRVGLARAITA 190

Query: 182 NPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHDLDEAMRIGDRIAIMQNG 241
           +P+++LMDE FSALDPLIR ++QDE  +L  +  ++ VFI+HDLDEA+RIGDRIAIM++G
Sbjct: 191 DPEVILMDEPFSALDPLIRRQLQDEFRQLTKELGKSAVFITHDLDEAIRIGDRIAIMKDG 250

Query: 242 EVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIARRSPVGLIR-KTPGFGPRSAL 300
            ++QVGT +EI+ NPA+DYV  F  G+    +  A  +   +PV   +   PG      +
Sbjct: 251 AIIQVGTAEEIVLNPADDYVAEFVAGISRLHLVRANSV--MTPVESFKVANPGCDIARLI 308

Query: 301 KLLQDEDREYGYVIERGNKFVGVVSIDSLKAALSQAQGIEAALIDDPLVVDAQTP 355
           K   D D          N+ +G +++ S + AL        A++D+ +VV   TP
Sbjct: 309 KTSVDADI---------NELIG-LTMKSERDAL--------AVVDNGVVVGIITP 345


Lambda     K      H
   0.319    0.137    0.378 

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: 417
Number of extensions: 19
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 400
Length of database: 372
Length adjustment: 30
Effective length of query: 370
Effective length of database: 342
Effective search space:   126540
Effective search space used:   126540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 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