GapMind for catabolism of small carbon sources

 

Aligments for a candidate for proV in Pseudomonas fluorescens FW300-N1B4

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate Pf1N1B4_2261 Putrescine transport ATP-binding protein PotG (TC 3.A.1.11.2)

Query= SwissProt::P17328
         (400 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2261 Putrescine transport
           ATP-binding protein PotG (TC 3.A.1.11.2)
          Length = 380

 Score =  187 bits (474), Expect = 6e-52
 Identities = 107/266 (40%), 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  DRVTKKFDETIAVDDVSLEIKKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLDGVD 85

Query: 92  IAKISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQ 151
           I  +   E      + I M+FQS+AL PHMTV  N AFG++   + A E   +  D L+ 
Sbjct: 86  ITDMPPYE------RPINMMFQSYALFPHMTVAQNIAFGLKQDKLPAAEVDARVADMLKL 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 AKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDI- 270
            +   T V ++HD +EAM + +RIAIM  G + Q+G+P +I   P +  V  F   V+I 
Sbjct: 200 ERVGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQIGSPIDIYETPTSRLVCEFIGNVNIF 259

Query: 271 ----------SQVFSAKDIARRSPVG 286
                       + + KD+ R+  VG
Sbjct: 260 DGEVIDDAEGHAIITCKDLDRQIYVG 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: 336
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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