GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proV in Methylocystis bryophila S285

Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_245300279.1 B1812_RS18275 sulfate/molybdate ABC transporter ATP-binding protein

Query= SwissProt::P17328
         (400 letters)



>NCBI__GCF_002117405.1:WP_245300279.1
          Length = 353

 Score =  167 bits (423), Expect = 4e-46
 Identities = 89/225 (39%), Positives = 139/225 (61%), Gaps = 10/225 (4%)

Query: 44  VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103
           ++D SL I  GE+  ++G SGSGK+T++R++  L  P RG V  D ++   +S      V
Sbjct: 14  LRDVSLDIAGGELVALLGPSGSGKTTLLRVIAGLNSPHRGAVFFDALNATSLS------V 67

Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGIAAQE-RRE---KALDALRQVGLENYAH 159
           + +++  VFQ++AL  HM+V DN AFG++    A++  +RE   +  + L  V LE    
Sbjct: 68  QERRVGFVFQNYALFKHMSVADNVAFGLKARPRASRPPKREIAARVAELLELVQLEGLGQ 127

Query: 160 AYPDELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIV 219
            YP +LSGG RQRV LARALAI P +LL+DE F ALD  +R +++  L ++  +   T V
Sbjct: 128 RYPAQLSGGQRQRVALARALAIEPRVLLLDEPFGALDARVRKDLRRWLREIHKRTGLTTV 187

Query: 220 FISHDLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTF 264
           F++HD DEAM + DR+ ++  G + Q G+P  + + PA+ +V +F
Sbjct: 188 FVTHDQDEAMELADRVVVLNQGRIEQAGSPAALYDRPASAFVLSF 232


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: 321
Number of extensions: 20
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: 353
Length adjustment: 30
Effective length of query: 370
Effective length of database: 323
Effective search space:   119510
Effective search space used:   119510
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 Apr 09 2024. 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