GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Dechlorosoma suillum PS

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>FitnessBrowser__PS:Dsui_0258
          Length = 360

 Score =  174 bits (441), Expect = 4e-48
 Identities = 91/241 (37%), Positives = 146/241 (60%), Gaps = 10/241 (4%)

Query: 34  ILEKTGLSLGVKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIA 93
           I ++ G  + + D SL+I  GE+  ++G SG GK+T++R++  +     GQV+ +G    
Sbjct: 8   IAKRFGNFVALDDVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEG---- 63

Query: 94  KISDAELREVRRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQ----ERREKALDAL 149
             S+A     R +++  VFQ +AL  HM V +N AFG+ +     +    E R++ +D L
Sbjct: 64  --SEATHLHARERQVGFVFQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLL 121

Query: 150 RQVGLENYAHAYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVK 209
             V L+  A  YP +LSGG RQR+ LARALA+ P +LL+DE F ALD  +R E++  L +
Sbjct: 122 SLVQLDWLADRYPTQLSGGQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRR 181

Query: 210 LQAKHQRTIVFISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGVD 269
           L  +   + VF++HD +EA+ + DR+ +M  G + QVG+PDE+ +NPA+ +V  F   V+
Sbjct: 182 LHDEMHISSVFVTHDQEEALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGNVN 241

Query: 270 I 270
           +
Sbjct: 242 V 242


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: 306
Number of extensions: 19
Number of successful extensions: 3
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: 360
Length adjustment: 30
Effective length of query: 370
Effective length of database: 330
Effective search space:   122100
Effective search space used:   122100
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