GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Pseudomonas fluorescens FW300-N2E3

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate AO353_08570 AO353_08570 transporter

Query= SwissProt::P17328
         (400 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08570
          Length = 380

 Score =  185 bits (470), Expect = 2e-51
 Identities = 106/266 (39%), Positives = 158/266 (59%), Gaps = 17/266 (6%)

Query: 32  EQILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVD 91
           +++ +K   ++ V D SL I +GEIF ++G SGSGKST++R+L     PT G++ +DGVD
Sbjct: 26  DRVTKKFDETIAVDDVSLEIRKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIFLDGVD 85

Query: 92  IAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQ 151
           I ++   E      + I M+FQS+AL PHMTV  N AFG++   I + E   +  + L+ 
Sbjct: 86  ITEMPPYE------RPINMMFQSYALFPHMTVAQNIAFGLKQDKIPSAEVDARVTEMLKL 139

Query: 152 VGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQ 211
           V +  YA   P +LSGG RQRV LAR+LA  P +LL+DE   ALD  +R++MQ ELV++ 
Sbjct: 140 VQMSQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEII 199

Query: 212 AKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDIS 271
            +   T V ++HD +EAM + +RIAIM  G + Q+G+P +I   P +  V  F   V+I 
Sbjct: 200 ERVGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQIGSPIDIYETPTSRLVCEFIGNVNIF 259

Query: 272 Q-----------VFSAKDIARRSPVG 286
           +           + + KD+ R   VG
Sbjct: 260 EGEVVDDAEGHALITCKDLDRNIYVG 285


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: 332
Number of extensions: 16
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: 400
Length of database: 380
Length adjustment: 30
Effective length of query: 370
Effective length of database: 350
Effective search space:   129500
Effective search space used:   129500
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:

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