GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Escherichia coli BW25113

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate 15248 b1126 putrescine/spermidine ABC transporter ATPase protein (NCBI)

Query= SwissProt::P17328
         (400 letters)



>FitnessBrowser__Keio:15248
          Length = 378

 Score =  174 bits (440), Expect = 5e-48
 Identities = 99/238 (41%), Positives = 143/238 (60%), Gaps = 9/238 (3%)

Query: 44  VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103
           +    L I  GE   ++G SG GK+T++RL+  L     G++++D  DI  +  AE R V
Sbjct: 33  IPQLDLTINNGEFLTLLGPSGCGKTTVLRLIAGLETVDSGRIMLDNEDITHVP-AENRYV 91

Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQERREKALDALRQVGLENYAHAYPD 163
                  VFQS+AL PHMTV +N AFG+ +    A E   + ++ALR V LE +A   P 
Sbjct: 92  NT-----VFQSYALFPHMTVFENVAFGLRMQKTPAAEITPRVMEALRMVQLETFAQRKPH 146

Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223
           +LSGG +QRV +ARA+   P +LL+DE+ SALD  +R +MQ+EL  LQ K   T VF++H
Sbjct: 147 QLSGGQQQRVAIARAVVNKPRLLLLDESLSALDYKLRKQMQNELKALQRKLGITFVFVTH 206

Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVDISQVFSAKDIAR 281
           D +EA+ + DRI +M++G + Q GTP EI   P N +V  F   ++   +F+A  I R
Sbjct: 207 DQEEALTMSDRIVVMRDGRIEQDGTPREIYEEPKNLFVAGFIGEIN---MFNATVIER 261


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: 330
Number of extensions: 13
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: 378
Length adjustment: 30
Effective length of query: 370
Effective length of database: 348
Effective search space:   128760
Effective search space used:   128760
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